Starting phenix.real_space_refine on Thu Mar 5 14:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nd0_0439/03_2026/6nd0_0439.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nd0_0439/03_2026/6nd0_0439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nd0_0439/03_2026/6nd0_0439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nd0_0439/03_2026/6nd0_0439.map" model { file = "/net/cci-nas-00/data/ceres_data/6nd0_0439/03_2026/6nd0_0439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nd0_0439/03_2026/6nd0_0439.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 156 5.16 5 C 14736 2.51 5 N 3792 2.21 5 O 4280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Chain: "C" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Chain: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5741 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 702} Chain breaks: 2 Time building chain proxies: 5.74, per 1000 atoms: 0.25 Number of scatterers: 22964 At special positions: 0 Unit cell: (140.448, 140.448, 130.944, 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 156 16.00 O 4280 8.00 N 3792 7.00 C 14736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5504 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 18 sheets defined 42.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 229 through 260 removed outlier: 4.343A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.296A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 322 removed outlier: 4.213A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 353 through 364 removed outlier: 4.342A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.894A pdb=" N VAL A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.582A pdb=" N TYR A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.534A pdb=" N GLY A 480 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 498 removed outlier: 3.747A pdb=" N ALA A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.550A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.524A pdb=" N PHE A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.598A pdb=" N ALA A 608 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 798 through 801 removed outlier: 3.670A pdb=" N ALA A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 805 through 809 removed outlier: 3.878A pdb=" N LEU A 809 " --> pdb=" O TYR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 removed outlier: 4.680A pdb=" N ARG A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 850 removed outlier: 3.589A pdb=" N ALA A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.555A pdb=" N CYS A 855 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.615A pdb=" N ILE A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 950 removed outlier: 3.613A pdb=" N GLN A 947 " --> pdb=" O THR A 944 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 949 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 950 " --> pdb=" O GLN A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 980 through 988 removed outlier: 3.777A pdb=" N PHE A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 988 " --> pdb=" O ALA A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 992 removed outlier: 3.847A pdb=" N LEU A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 989 through 992' Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.894A pdb=" N THR A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1014 removed outlier: 3.831A pdb=" N LEU A1010 " --> pdb=" O GLU A1006 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1029 Processing helix chain 'A' and resid 1042 through 1046 removed outlier: 4.136A pdb=" N PHE A1045 " --> pdb=" O ASP A1042 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1046 " --> pdb=" O GLY A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1042 through 1046' Processing helix chain 'A' and resid 1053 through 1065 removed outlier: 3.662A pdb=" N CYS A1059 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1062 " --> pdb=" O PHE A1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 260 removed outlier: 4.344A pdb=" N LEU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.296A pdb=" N TYR B 279 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 322 removed outlier: 4.212A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 353 through 364 removed outlier: 4.342A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.894A pdb=" N VAL B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.583A pdb=" N TYR B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.534A pdb=" N GLY B 480 " --> pdb=" O TRP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 498 removed outlier: 3.746A pdb=" N ALA B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.550A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.525A pdb=" N PHE B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.599A pdb=" N ALA B 608 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 771 Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 798 through 801 removed outlier: 3.669A pdb=" N ALA B 801 " --> pdb=" O PRO B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 798 through 801' Processing helix chain 'B' and resid 805 through 809 removed outlier: 3.878A pdb=" N LEU B 809 " --> pdb=" O TYR B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 removed outlier: 4.680A pdb=" N ARG B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 824 " --> pdb=" O TYR B 820 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU B 826 " --> pdb=" O LYS B 822 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N THR B 827 " --> pdb=" O ARG B 823 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 828 " --> pdb=" O GLU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 850 removed outlier: 3.589A pdb=" N ALA B 849 " --> pdb=" O ALA B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.555A pdb=" N CYS B 855 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 886 removed outlier: 3.616A pdb=" N ILE B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 950 removed outlier: 3.613A pdb=" N GLN B 947 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 949 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 950 " --> pdb=" O GLN B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 969 Processing helix chain 'B' and resid 976 through 979 Processing helix chain 'B' and resid 980 through 988 removed outlier: 3.777A pdb=" N PHE B 987 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN B 988 " --> pdb=" O ALA B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1001 removed outlier: 3.675A pdb=" N ILE B 995 " --> pdb=" O ILE B 991 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1014 removed outlier: 3.832A pdb=" N LEU B1010 " --> pdb=" O GLU B1006 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B1014 " --> pdb=" O LEU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1029 Processing helix chain 'B' and resid 1042 through 1046 removed outlier: 4.137A pdb=" N PHE B1045 " --> pdb=" O ASP B1042 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B1046 " --> pdb=" O GLY B1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1042 through 1046' Processing helix chain 'B' and resid 1053 through 1065 removed outlier: 3.663A pdb=" N CYS B1059 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B1062 " --> pdb=" O PHE B1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.903A pdb=" N LEU C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 250 " --> pdb=" O TRP C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 273 through 286 removed outlier: 4.089A pdb=" N CYS C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 279 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.904A pdb=" N MET C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.517A pdb=" N ILE C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.643A pdb=" N VAL C 356 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 removed outlier: 3.615A pdb=" N LEU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 449 removed outlier: 3.556A pdb=" N ASP C 437 " --> pdb=" O PRO C 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 447 " --> pdb=" O ARG C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.847A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 472 " --> pdb=" O HIS C 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 467 through 472' Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.647A pdb=" N GLY C 480 " --> pdb=" O TRP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 498 removed outlier: 3.622A pdb=" N LEU C 489 " --> pdb=" O CYS C 485 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.502A pdb=" N TYR C 528 " --> pdb=" O TRP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.615A pdb=" N PHE C 545 " --> pdb=" O SER C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 560 removed outlier: 3.532A pdb=" N GLU C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 556 " --> pdb=" O THR C 552 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 558 " --> pdb=" O CYS C 554 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 559 " --> pdb=" O GLU C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 609 removed outlier: 3.649A pdb=" N LYS C 606 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.571A pdb=" N ILE C 762 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 771 removed outlier: 3.592A pdb=" N MET C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 798 through 800 No H-bonds generated for 'chain 'C' and resid 798 through 800' Processing helix chain 'C' and resid 817 through 825 removed outlier: 4.483A pdb=" N ARG C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 824 " --> pdb=" O TYR C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 828 No H-bonds generated for 'chain 'C' and resid 826 through 828' Processing helix chain 'C' and resid 843 through 850 removed outlier: 3.546A pdb=" N VAL C 850 " --> pdb=" O ASP C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 Processing helix chain 'C' and resid 875 through 886 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.783A pdb=" N ASN C 945 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN C 947 " --> pdb=" O THR C 944 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 950 " --> pdb=" O GLN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 969 removed outlier: 3.506A pdb=" N ALA C 968 " --> pdb=" O THR C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 979 Processing helix chain 'C' and resid 980 through 988 removed outlier: 3.594A pdb=" N PHE C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 996 removed outlier: 3.717A pdb=" N THR C 993 " --> pdb=" O ASP C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1013 removed outlier: 3.611A pdb=" N LEU C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1050 removed outlier: 4.333A pdb=" N ASP C1050 " --> pdb=" O ALA C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1065 removed outlier: 3.767A pdb=" N CYS C1059 " --> pdb=" O GLY C1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 252 removed outlier: 3.904A pdb=" N LEU D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 250 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 273 through 286 removed outlier: 4.088A pdb=" N CYS D 277 " --> pdb=" O THR D 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 279 " --> pdb=" O TRP D 275 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 316 removed outlier: 3.903A pdb=" N MET D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 305 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.517A pdb=" N ILE D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 removed outlier: 3.643A pdb=" N VAL D 356 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 removed outlier: 3.615A pdb=" N LEU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 449 removed outlier: 3.554A pdb=" N ASP D 437 " --> pdb=" O PRO D 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 447 " --> pdb=" O ARG D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 466 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.848A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 472 " --> pdb=" O HIS D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 467 through 472' Processing helix chain 'D' and resid 476 through 480 removed outlier: 3.647A pdb=" N GLY D 480 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 498 removed outlier: 3.623A pdb=" N LEU D 489 " --> pdb=" O CYS D 485 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 491 " --> pdb=" O ALA D 487 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 524 through 529 removed outlier: 3.502A pdb=" N TYR D 528 " --> pdb=" O TRP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.615A pdb=" N PHE D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 560 removed outlier: 3.533A pdb=" N GLU D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU D 556 " --> pdb=" O THR D 552 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 558 " --> pdb=" O CYS D 554 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 559 " --> pdb=" O GLU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 609 removed outlier: 3.650A pdb=" N LYS D 606 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 762 removed outlier: 3.571A pdb=" N ILE D 762 " --> pdb=" O GLU D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 771 removed outlier: 3.592A pdb=" N MET D 770 " --> pdb=" O SER D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 Processing helix chain 'D' and resid 798 through 800 No H-bonds generated for 'chain 'D' and resid 798 through 800' Processing helix chain 'D' and resid 817 through 825 removed outlier: 4.482A pdb=" N ARG D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 824 " --> pdb=" O TYR D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 828 No H-bonds generated for 'chain 'D' and resid 826 through 828' Processing helix chain 'D' and resid 843 through 850 removed outlier: 3.546A pdb=" N VAL D 850 " --> pdb=" O ASP D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 855 Processing helix chain 'D' and resid 875 through 886 Processing helix chain 'D' and resid 942 through 950 removed outlier: 3.783A pdb=" N ASN D 945 " --> pdb=" O ASN D 942 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 947 " --> pdb=" O THR D 944 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 950 " --> pdb=" O GLN D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 969 removed outlier: 3.506A pdb=" N ALA D 968 " --> pdb=" O THR D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 979 Processing helix chain 'D' and resid 980 through 988 removed outlier: 3.594A pdb=" N PHE D 987 " --> pdb=" O SER D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 996 removed outlier: 3.718A pdb=" N THR D 993 " --> pdb=" O ASP D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1013 removed outlier: 3.611A pdb=" N LEU D1010 " --> pdb=" O GLU D1006 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D1013 " --> pdb=" O ALA D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1050 removed outlier: 4.333A pdb=" N ASP D1050 " --> pdb=" O ALA D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1065 removed outlier: 3.767A pdb=" N CYS D1059 " --> pdb=" O GLY D1055 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.252A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.785A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 744 through 745 removed outlier: 4.483A pdb=" N TYR A 744 " --> pdb=" O GLY A1020 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A1020 " --> pdb=" O TYR A 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 834 through 838 removed outlier: 6.352A pdb=" N ILE A 812 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 837 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE A 814 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 782 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER A 862 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE A 973 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR A 938 " --> pdb=" O PHE A 973 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1036 through 1039 removed outlier: 3.599A pdb=" N ALA A1036 " --> pdb=" O CYS A1109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A1106 " --> pdb=" O TYR A1073 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A1071 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 398 through 399 removed outlier: 7.252A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 535 through 540 removed outlier: 3.784A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 744 through 745 removed outlier: 4.483A pdb=" N TYR B 744 " --> pdb=" O GLY B1020 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B1020 " --> pdb=" O TYR B 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 834 through 838 removed outlier: 6.352A pdb=" N ILE B 812 " --> pdb=" O SER B 835 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU B 837 " --> pdb=" O ILE B 812 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE B 814 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 782 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER B 862 " --> pdb=" O GLU B 939 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE B 973 " --> pdb=" O ILE B 936 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR B 938 " --> pdb=" O PHE B 973 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1036 through 1039 removed outlier: 3.599A pdb=" N ALA B1036 " --> pdb=" O CYS B1109 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B1106 " --> pdb=" O TYR B1073 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B1071 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 398 through 401 removed outlier: 4.059A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.166A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 834 through 838 removed outlier: 6.126A pdb=" N ILE C 812 " --> pdb=" O SER C 835 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C 837 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE C 814 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 777 " --> pdb=" O VAL C 813 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 815 " --> pdb=" O VAL C 777 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 779 " --> pdb=" O VAL C 815 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER C 862 " --> pdb=" O GLU C 939 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE C 973 " --> pdb=" O ILE C 936 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 938 " --> pdb=" O PHE C 973 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1036 through 1039 removed outlier: 3.976A pdb=" N ALA C1036 " --> pdb=" O CYS C1109 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C1071 " --> pdb=" O PHE C1108 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 398 through 401 removed outlier: 4.059A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.167A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 834 through 838 removed outlier: 6.127A pdb=" N ILE D 812 " --> pdb=" O SER D 835 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU D 837 " --> pdb=" O ILE D 812 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE D 814 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL D 777 " --> pdb=" O VAL D 813 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL D 815 " --> pdb=" O VAL D 777 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 779 " --> pdb=" O VAL D 815 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER D 862 " --> pdb=" O GLU D 939 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE D 973 " --> pdb=" O ILE D 936 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 938 " --> pdb=" O PHE D 973 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1036 through 1039 removed outlier: 3.976A pdb=" N ALA D1036 " --> pdb=" O CYS D1109 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D1071 " --> pdb=" O PHE D1108 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7242 1.34 - 1.46: 4472 1.46 - 1.57: 11514 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 23452 Sorted by residual: bond pdb=" CB ASN B 803 " pdb=" CG ASN B 803 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" CB ASN A 803 " pdb=" CG ASN A 803 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" C VAL A1102 " pdb=" N PRO A1103 " ideal model delta sigma weight residual 1.337 1.354 -0.017 9.80e-03 1.04e+04 3.17e+00 bond pdb=" C VAL B1102 " pdb=" N PRO B1103 " ideal model delta sigma weight residual 1.337 1.354 -0.017 9.80e-03 1.04e+04 3.17e+00 bond pdb=" CB VAL D 999 " pdb=" CG1 VAL D 999 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 ... (remaining 23447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 30306 1.94 - 3.89: 1270 3.89 - 5.83: 182 5.83 - 7.77: 38 7.77 - 9.72: 20 Bond angle restraints: 31816 Sorted by residual: angle pdb=" C ASP C 745 " pdb=" N SER C 746 " pdb=" CA SER C 746 " ideal model delta sigma weight residual 121.54 131.25 -9.71 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C ASP D 745 " pdb=" N SER D 746 " pdb=" CA SER D 746 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C LEU C1041 " pdb=" N ASP C1042 " pdb=" CA ASP C1042 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C LEU D1041 " pdb=" N ASP D1042 " pdb=" CA ASP D1042 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N SER C 746 " pdb=" CA SER C 746 " pdb=" C SER C 746 " ideal model delta sigma weight residual 110.80 119.90 -9.10 2.13e+00 2.20e-01 1.82e+01 ... (remaining 31811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 13293 17.30 - 34.60: 587 34.60 - 51.89: 81 51.89 - 69.19: 15 69.19 - 86.49: 12 Dihedral angle restraints: 13988 sinusoidal: 5476 harmonic: 8512 Sorted by residual: dihedral pdb=" CA GLU D 960 " pdb=" C GLU D 960 " pdb=" N LEU D 961 " pdb=" CA LEU D 961 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLU C 960 " pdb=" C GLU C 960 " pdb=" N LEU C 961 " pdb=" CA LEU C 961 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA CYS D1069 " pdb=" C CYS D1069 " pdb=" N PHE D1070 " pdb=" CA PHE D1070 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 13985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2529 0.056 - 0.112: 921 0.112 - 0.168: 169 0.168 - 0.224: 33 0.224 - 0.281: 8 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CB ILE A 579 " pdb=" CA ILE A 579 " pdb=" CG1 ILE A 579 " pdb=" CG2 ILE A 579 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE B 416 " pdb=" CA ILE B 416 " pdb=" CG1 ILE B 416 " pdb=" CG2 ILE B 416 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3657 not shown) Planarity restraints: 4040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO B 320 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 320 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C PHE A1099 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A1100 " -0.014 2.00e-02 2.50e+03 ... (remaining 4037 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1355 2.72 - 3.27: 22519 3.27 - 3.81: 36671 3.81 - 4.36: 46195 4.36 - 4.90: 77456 Nonbonded interactions: 184196 Sorted by model distance: nonbonded pdb=" O TYR C 744 " pdb=" OD1 ASP C 745 " model vdw 2.178 3.040 nonbonded pdb=" O TYR D 744 " pdb=" OD1 ASP D 745 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR B 336 " pdb=" OE1 GLU B 374 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR A 336 " pdb=" OE1 GLU A 374 " model vdw 2.274 3.040 nonbonded pdb=" O GLY B 531 " pdb=" OG1 THR B1093 " model vdw 2.275 3.040 ... (remaining 184191 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.690 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 23452 Z= 0.358 Angle : 0.939 9.717 31816 Z= 0.506 Chirality : 0.059 0.281 3660 Planarity : 0.006 0.062 4040 Dihedral : 10.798 86.490 8484 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.96 % Rotamer: Outliers : 0.43 % Allowed : 3.61 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.62 (0.13), residues: 2884 helix: -4.36 (0.08), residues: 1022 sheet: -2.08 (0.24), residues: 388 loop : -2.29 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1076 TYR 0.038 0.003 TYR B1073 PHE 0.031 0.003 PHE D1070 TRP 0.027 0.004 TRP D 825 HIS 0.010 0.002 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00833 (23452) covalent geometry : angle 0.93871 (31816) hydrogen bonds : bond 0.31497 ( 659) hydrogen bonds : angle 10.46220 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 533 time to evaluate : 0.875 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: A 238 LEU cc_start: 0.7180 (mt) cc_final: 0.6863 (mm) REVERT: A 242 PHE cc_start: 0.8382 (m-80) cc_final: 0.7819 (m-80) REVERT: A 279 TYR cc_start: 0.6537 (t80) cc_final: 0.6079 (t80) REVERT: A 290 TYR cc_start: 0.6687 (m-80) cc_final: 0.5702 (m-80) REVERT: A 314 MET cc_start: 0.7925 (mtt) cc_final: 0.7193 (tpt) REVERT: A 361 LYS cc_start: 0.8499 (mttt) cc_final: 0.7975 (tppt) REVERT: A 437 ASP cc_start: 0.8916 (t70) cc_final: 0.8496 (t0) REVERT: A 506 MET cc_start: 0.8769 (tpt) cc_final: 0.8476 (tpp) REVERT: A 517 ILE cc_start: 0.8443 (pt) cc_final: 0.8222 (tt) REVERT: A 526 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7354 (pttt) REVERT: A 603 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7687 (tmtt) REVERT: A 610 PHE cc_start: 0.7860 (m-80) cc_final: 0.7580 (m-10) REVERT: A 752 TRP cc_start: 0.8689 (t60) cc_final: 0.8486 (t60) REVERT: A 767 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 793 ARG cc_start: 0.8386 (ttp-110) cc_final: 0.7995 (ttm-80) REVERT: A 797 MET cc_start: 0.8358 (mtm) cc_final: 0.8112 (mtt) REVERT: A 824 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 856 ASP cc_start: 0.7595 (m-30) cc_final: 0.7128 (t0) REVERT: A 857 MET cc_start: 0.8534 (tpp) cc_final: 0.8240 (tpt) REVERT: B 238 LEU cc_start: 0.7180 (mt) cc_final: 0.6863 (mm) REVERT: B 242 PHE cc_start: 0.8381 (m-80) cc_final: 0.7819 (m-80) REVERT: B 279 TYR cc_start: 0.6537 (t80) cc_final: 0.6075 (t80) REVERT: B 290 TYR cc_start: 0.6689 (m-80) cc_final: 0.5719 (m-80) REVERT: B 314 MET cc_start: 0.7924 (mtt) cc_final: 0.7190 (tpt) REVERT: B 361 LYS cc_start: 0.8493 (mttt) cc_final: 0.7982 (tppt) REVERT: B 437 ASP cc_start: 0.8911 (t70) cc_final: 0.8336 (t0) REVERT: B 506 MET cc_start: 0.8772 (tpt) cc_final: 0.8469 (tpp) REVERT: B 517 ILE cc_start: 0.8442 (pt) cc_final: 0.8221 (tt) REVERT: B 526 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7359 (pttt) REVERT: B 603 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7660 (tmtt) REVERT: B 610 PHE cc_start: 0.7853 (m-80) cc_final: 0.7604 (m-10) REVERT: B 767 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 793 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7993 (ttm-80) REVERT: B 797 MET cc_start: 0.8354 (mtm) cc_final: 0.8115 (mtt) REVERT: B 824 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 856 ASP cc_start: 0.7598 (m-30) cc_final: 0.7128 (t0) REVERT: B 857 MET cc_start: 0.8540 (tpp) cc_final: 0.8245 (tpt) REVERT: B 1017 LEU cc_start: 0.8325 (mt) cc_final: 0.8100 (mt) REVERT: C 275 TRP cc_start: 0.4514 (p90) cc_final: 0.4294 (m-90) REVERT: C 286 SER cc_start: 0.7866 (m) cc_final: 0.7356 (t) REVERT: C 303 PHE cc_start: 0.7567 (m-10) cc_final: 0.7306 (m-80) REVERT: C 304 MET cc_start: 0.7135 (ppp) cc_final: 0.5861 (mtt) REVERT: C 306 PHE cc_start: 0.7838 (t80) cc_final: 0.7225 (t80) REVERT: C 314 MET cc_start: 0.3575 (mmt) cc_final: 0.3207 (mmt) REVERT: C 442 MET cc_start: 0.9077 (mmm) cc_final: 0.8873 (mmm) REVERT: C 513 MET cc_start: 0.7843 (mmm) cc_final: 0.7532 (mmt) REVERT: C 569 GLU cc_start: 0.8056 (tt0) cc_final: 0.7267 (pp20) REVERT: C 604 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8232 (tp30) REVERT: C 824 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8250 (tp30) REVERT: C 856 ASP cc_start: 0.8055 (m-30) cc_final: 0.7355 (t0) REVERT: C 857 MET cc_start: 0.8650 (tpp) cc_final: 0.8247 (tpt) REVERT: C 888 MET cc_start: 0.9120 (mtp) cc_final: 0.8800 (mtp) REVERT: C 955 ASP cc_start: 0.7185 (m-30) cc_final: 0.6533 (p0) REVERT: C 980 SER cc_start: 0.8920 (p) cc_final: 0.8695 (m) REVERT: C 983 SER cc_start: 0.9083 (m) cc_final: 0.8483 (p) REVERT: C 991 ILE cc_start: 0.8782 (mm) cc_final: 0.8568 (mm) REVERT: C 1029 ASN cc_start: 0.7791 (m110) cc_final: 0.7436 (m-40) REVERT: D 275 TRP cc_start: 0.4515 (p90) cc_final: 0.4308 (m-90) REVERT: D 286 SER cc_start: 0.7861 (m) cc_final: 0.7347 (t) REVERT: D 303 PHE cc_start: 0.7599 (m-10) cc_final: 0.7319 (m-80) REVERT: D 304 MET cc_start: 0.7124 (ppp) cc_final: 0.5849 (mtt) REVERT: D 306 PHE cc_start: 0.7838 (t80) cc_final: 0.7230 (t80) REVERT: D 314 MET cc_start: 0.3551 (mmt) cc_final: 0.3191 (mmt) REVERT: D 442 MET cc_start: 0.9079 (mmm) cc_final: 0.8875 (mmm) REVERT: D 513 MET cc_start: 0.7839 (mmm) cc_final: 0.7530 (mmt) REVERT: D 569 GLU cc_start: 0.8056 (tt0) cc_final: 0.7261 (pp20) REVERT: D 604 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8211 (tp30) REVERT: D 824 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8276 (tp30) REVERT: D 856 ASP cc_start: 0.8058 (m-30) cc_final: 0.7456 (t0) REVERT: D 857 MET cc_start: 0.8656 (tpp) cc_final: 0.8280 (tpt) REVERT: D 888 MET cc_start: 0.9126 (mtp) cc_final: 0.8809 (mtp) REVERT: D 955 ASP cc_start: 0.7178 (m-30) cc_final: 0.6536 (p0) REVERT: D 980 SER cc_start: 0.8918 (p) cc_final: 0.8693 (m) REVERT: D 983 SER cc_start: 0.9080 (m) cc_final: 0.8476 (p) REVERT: D 991 ILE cc_start: 0.8799 (mm) cc_final: 0.8585 (mm) REVERT: D 1029 ASN cc_start: 0.7825 (m110) cc_final: 0.7471 (m-40) outliers start: 11 outliers final: 2 residues processed: 542 average time/residue: 0.1707 time to fit residues: 140.7638 Evaluate side-chains 287 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 991 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 268 ASN A 384 ASN A 451 HIS A 616 HIS A 803 ASN A 867 ASN A1079 HIS B 237 ASN B 268 ASN B 384 ASN B 451 HIS B 616 HIS B 803 ASN B 867 ASN B 874 GLN B1079 HIS C 379 HIS C 427 ASN C 459 GLN C 534 ASN C 585 ASN C 811 HIS C 874 GLN C 942 ASN D 379 HIS D 427 ASN D 459 GLN D 534 ASN D 585 ASN D 811 HIS D 874 GLN D 942 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.145618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108759 restraints weight = 42906.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111977 restraints weight = 24268.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113875 restraints weight = 17395.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115316 restraints weight = 14375.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116160 restraints weight = 12586.245| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23452 Z= 0.165 Angle : 0.639 9.062 31816 Z= 0.341 Chirality : 0.045 0.281 3660 Planarity : 0.005 0.048 4040 Dihedral : 6.447 80.553 3120 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.10 % Favored : 93.79 % Rotamer: Outliers : 1.69 % Allowed : 7.46 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.14), residues: 2884 helix: -3.04 (0.12), residues: 1078 sheet: -1.59 (0.25), residues: 396 loop : -1.85 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 823 TYR 0.021 0.002 TYR C1073 PHE 0.028 0.002 PHE A1058 TRP 0.025 0.002 TRP D 752 HIS 0.006 0.001 HIS A1079 Details of bonding type rmsd covalent geometry : bond 0.00369 (23452) covalent geometry : angle 0.63863 (31816) hydrogen bonds : bond 0.05825 ( 659) hydrogen bonds : angle 5.98434 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 336 time to evaluate : 0.835 Fit side-chains REVERT: A 238 LEU cc_start: 0.7332 (mt) cc_final: 0.6985 (mm) REVERT: A 242 PHE cc_start: 0.8174 (m-80) cc_final: 0.7879 (m-80) REVERT: A 279 TYR cc_start: 0.6283 (t80) cc_final: 0.6009 (t80) REVERT: A 290 TYR cc_start: 0.6629 (m-80) cc_final: 0.5919 (m-80) REVERT: A 314 MET cc_start: 0.7775 (mtt) cc_final: 0.7074 (tpt) REVERT: A 526 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7912 (pttt) REVERT: A 824 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7288 (tp30) REVERT: B 238 LEU cc_start: 0.7330 (mt) cc_final: 0.6988 (mm) REVERT: B 242 PHE cc_start: 0.8177 (m-80) cc_final: 0.7880 (m-80) REVERT: B 279 TYR cc_start: 0.6279 (t80) cc_final: 0.5999 (t80) REVERT: B 290 TYR cc_start: 0.6648 (m-80) cc_final: 0.6008 (m-80) REVERT: B 314 MET cc_start: 0.7769 (mtt) cc_final: 0.7072 (tpt) REVERT: B 437 ASP cc_start: 0.8480 (t70) cc_final: 0.8223 (t0) REVERT: B 526 LYS cc_start: 0.8423 (ttpt) cc_final: 0.7911 (pttt) REVERT: B 824 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7293 (tp30) REVERT: C 285 MET cc_start: 0.7265 (ptm) cc_final: 0.7019 (ptt) REVERT: C 286 SER cc_start: 0.8229 (m) cc_final: 0.7612 (t) REVERT: C 303 PHE cc_start: 0.7725 (m-10) cc_final: 0.7340 (m-80) REVERT: C 304 MET cc_start: 0.6691 (ppp) cc_final: 0.5575 (mtt) REVERT: C 306 PHE cc_start: 0.7818 (t80) cc_final: 0.7265 (t80) REVERT: C 392 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8503 (mmmt) REVERT: C 522 ASP cc_start: 0.7044 (t0) cc_final: 0.6491 (t0) REVERT: C 553 VAL cc_start: 0.8835 (t) cc_final: 0.8536 (p) REVERT: C 955 ASP cc_start: 0.6469 (m-30) cc_final: 0.6069 (p0) REVERT: D 285 MET cc_start: 0.7202 (ptm) cc_final: 0.6966 (ptt) REVERT: D 286 SER cc_start: 0.8212 (m) cc_final: 0.7613 (t) REVERT: D 303 PHE cc_start: 0.7734 (m-10) cc_final: 0.7344 (m-80) REVERT: D 304 MET cc_start: 0.6681 (ppp) cc_final: 0.5570 (mtt) REVERT: D 306 PHE cc_start: 0.7825 (t80) cc_final: 0.7280 (t80) REVERT: D 392 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8492 (mmmt) REVERT: D 522 ASP cc_start: 0.7027 (t0) cc_final: 0.6477 (t0) REVERT: D 553 VAL cc_start: 0.8832 (t) cc_final: 0.8551 (t) REVERT: D 955 ASP cc_start: 0.6473 (m-30) cc_final: 0.6073 (p0) outliers start: 43 outliers final: 18 residues processed: 370 average time/residue: 0.1616 time to fit residues: 92.4261 Evaluate side-chains 267 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 991 ILE Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 1048 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 252 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 794 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 ASN A 874 GLN B 372 ASN B 582 ASN ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 ASN C 459 GLN C1029 ASN D 459 GLN D1029 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109173 restraints weight = 43008.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112388 restraints weight = 24424.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114448 restraints weight = 17614.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115437 restraints weight = 14497.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116437 restraints weight = 13009.342| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23452 Z= 0.139 Angle : 0.590 8.719 31816 Z= 0.311 Chirality : 0.044 0.229 3660 Planarity : 0.004 0.045 4040 Dihedral : 5.853 73.798 3120 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.63 % Rotamer: Outliers : 2.24 % Allowed : 9.30 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.15), residues: 2884 helix: -2.39 (0.13), residues: 1084 sheet: -1.14 (0.26), residues: 396 loop : -1.52 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 607 TYR 0.016 0.001 TYR C 318 PHE 0.023 0.001 PHE D1070 TRP 0.030 0.003 TRP D 752 HIS 0.004 0.001 HIS A1079 Details of bonding type rmsd covalent geometry : bond 0.00312 (23452) covalent geometry : angle 0.59032 (31816) hydrogen bonds : bond 0.04242 ( 659) hydrogen bonds : angle 5.40415 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8180 (m-80) cc_final: 0.7463 (m-10) REVERT: A 279 TYR cc_start: 0.6347 (t80) cc_final: 0.5978 (t80) REVERT: A 290 TYR cc_start: 0.6705 (m-80) cc_final: 0.5925 (m-80) REVERT: A 314 MET cc_start: 0.7767 (mtt) cc_final: 0.6988 (tpp) REVERT: A 526 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7824 (pttt) REVERT: A 824 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 242 PHE cc_start: 0.8184 (m-80) cc_final: 0.7470 (m-10) REVERT: B 279 TYR cc_start: 0.6344 (t80) cc_final: 0.5963 (t80) REVERT: B 290 TYR cc_start: 0.6710 (m-80) cc_final: 0.5941 (m-80) REVERT: B 314 MET cc_start: 0.7769 (mtt) cc_final: 0.6988 (tpp) REVERT: B 437 ASP cc_start: 0.8569 (t70) cc_final: 0.8311 (t0) REVERT: B 526 LYS cc_start: 0.8405 (ttpt) cc_final: 0.7833 (pttt) REVERT: B 824 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7402 (tp30) REVERT: C 286 SER cc_start: 0.8022 (m) cc_final: 0.7518 (t) REVERT: C 303 PHE cc_start: 0.7806 (m-10) cc_final: 0.7581 (m-80) REVERT: C 304 MET cc_start: 0.6677 (ppp) cc_final: 0.5650 (mtt) REVERT: C 306 PHE cc_start: 0.7860 (t80) cc_final: 0.7328 (t80) REVERT: C 353 LEU cc_start: 0.8921 (tp) cc_final: 0.8713 (tt) REVERT: C 522 ASP cc_start: 0.6953 (t0) cc_final: 0.6402 (t0) REVERT: C 955 ASP cc_start: 0.6523 (m-30) cc_final: 0.6072 (p0) REVERT: C 1034 ARG cc_start: 0.3250 (pmm150) cc_final: 0.2074 (ptp90) REVERT: D 286 SER cc_start: 0.8014 (m) cc_final: 0.7503 (t) REVERT: D 303 PHE cc_start: 0.7808 (m-10) cc_final: 0.7583 (m-80) REVERT: D 304 MET cc_start: 0.6704 (ppp) cc_final: 0.5632 (mtt) REVERT: D 306 PHE cc_start: 0.7869 (t80) cc_final: 0.7336 (t80) REVERT: D 353 LEU cc_start: 0.8916 (tp) cc_final: 0.8706 (tt) REVERT: D 522 ASP cc_start: 0.6963 (t0) cc_final: 0.6416 (t0) REVERT: D 955 ASP cc_start: 0.6534 (m-30) cc_final: 0.6072 (p0) REVERT: D 1034 ARG cc_start: 0.3217 (pmm150) cc_final: 0.2038 (ptp90) outliers start: 57 outliers final: 47 residues processed: 328 average time/residue: 0.1458 time to fit residues: 76.5123 Evaluate side-chains 305 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 174 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 77 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN B 794 ASN ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN C 534 ASN ** C 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 534 ASN ** D 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.148623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113012 restraints weight = 42534.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117208 restraints weight = 25882.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117564 restraints weight = 16611.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119098 restraints weight = 16344.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119311 restraints weight = 14273.285| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23452 Z= 0.099 Angle : 0.524 7.759 31816 Z= 0.275 Chirality : 0.042 0.194 3660 Planarity : 0.004 0.040 4040 Dihedral : 5.272 67.029 3116 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.96 % Allowed : 10.48 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2884 helix: -1.83 (0.14), residues: 1072 sheet: -0.86 (0.27), residues: 394 loop : -1.28 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 607 TYR 0.014 0.001 TYR C 318 PHE 0.020 0.001 PHE D1070 TRP 0.029 0.002 TRP D 752 HIS 0.003 0.000 HIS A1079 Details of bonding type rmsd covalent geometry : bond 0.00211 (23452) covalent geometry : angle 0.52368 (31816) hydrogen bonds : bond 0.03405 ( 659) hydrogen bonds : angle 5.00100 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 302 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.6368 (t80) cc_final: 0.6051 (t80) REVERT: A 290 TYR cc_start: 0.6501 (m-80) cc_final: 0.5751 (m-80) REVERT: A 314 MET cc_start: 0.7790 (mtt) cc_final: 0.7576 (ppp) REVERT: A 526 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7701 (pttt) REVERT: A 569 GLU cc_start: 0.7484 (tp30) cc_final: 0.7257 (tp30) REVERT: A 824 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7347 (tp30) REVERT: B 279 TYR cc_start: 0.6367 (t80) cc_final: 0.6041 (t80) REVERT: B 290 TYR cc_start: 0.6596 (m-80) cc_final: 0.5868 (m-80) REVERT: B 314 MET cc_start: 0.7788 (mtt) cc_final: 0.7571 (ppp) REVERT: B 526 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7523 (pttt) REVERT: B 569 GLU cc_start: 0.7491 (tp30) cc_final: 0.7258 (tp30) REVERT: B 824 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7359 (tp30) REVERT: C 285 MET cc_start: 0.7220 (ptm) cc_final: 0.6985 (ptt) REVERT: C 286 SER cc_start: 0.8111 (m) cc_final: 0.7620 (t) REVERT: C 304 MET cc_start: 0.6515 (ppp) cc_final: 0.5494 (mtt) REVERT: C 522 ASP cc_start: 0.6738 (t0) cc_final: 0.6119 (t0) REVERT: C 955 ASP cc_start: 0.6431 (m-30) cc_final: 0.6012 (p0) REVERT: C 983 SER cc_start: 0.9017 (m) cc_final: 0.8717 (p) REVERT: C 1034 ARG cc_start: 0.3033 (pmm150) cc_final: 0.1934 (ptp90) REVERT: D 281 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5732 (tm) REVERT: D 285 MET cc_start: 0.7166 (ptm) cc_final: 0.6858 (ptt) REVERT: D 286 SER cc_start: 0.8176 (m) cc_final: 0.7664 (t) REVERT: D 303 PHE cc_start: 0.7701 (m-10) cc_final: 0.7500 (m-80) REVERT: D 304 MET cc_start: 0.6526 (ppp) cc_final: 0.5508 (mtt) REVERT: D 353 LEU cc_start: 0.8891 (tp) cc_final: 0.8675 (tt) REVERT: D 522 ASP cc_start: 0.6748 (t0) cc_final: 0.6137 (t0) REVERT: D 955 ASP cc_start: 0.6382 (m-30) cc_final: 0.6004 (p0) REVERT: D 983 SER cc_start: 0.9013 (m) cc_final: 0.8710 (p) REVERT: D 1034 ARG cc_start: 0.2948 (pmm150) cc_final: 0.1886 (ptp90) outliers start: 50 outliers final: 30 residues processed: 340 average time/residue: 0.1493 time to fit residues: 81.7388 Evaluate side-chains 296 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1038 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 246 optimal weight: 4.9990 chunk 232 optimal weight: 0.0870 chunk 243 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN D 231 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110762 restraints weight = 42501.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114021 restraints weight = 24011.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116148 restraints weight = 17241.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117384 restraints weight = 14090.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118241 restraints weight = 12459.030| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23452 Z= 0.122 Angle : 0.541 11.388 31816 Z= 0.279 Chirality : 0.044 0.192 3660 Planarity : 0.003 0.041 4040 Dihedral : 5.145 65.783 3116 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.32 % Allowed : 11.22 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2884 helix: -1.44 (0.15), residues: 1082 sheet: -0.81 (0.27), residues: 398 loop : -1.18 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 342 TYR 0.014 0.001 TYR C1073 PHE 0.022 0.001 PHE C1070 TRP 0.030 0.002 TRP D 752 HIS 0.004 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00278 (23452) covalent geometry : angle 0.54089 (31816) hydrogen bonds : bond 0.03249 ( 659) hydrogen bonds : angle 4.90271 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7939 (m-80) cc_final: 0.7652 (m-80) REVERT: A 279 TYR cc_start: 0.6472 (t80) cc_final: 0.6131 (t80) REVERT: A 290 TYR cc_start: 0.6777 (m-80) cc_final: 0.6024 (m-80) REVERT: A 304 MET cc_start: 0.8481 (ptt) cc_final: 0.7772 (mmt) REVERT: A 314 MET cc_start: 0.8039 (mtt) cc_final: 0.7138 (tpp) REVERT: A 460 MET cc_start: 0.8254 (mmt) cc_final: 0.7951 (mmt) REVERT: A 526 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7520 (pttt) REVERT: A 824 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7429 (tp30) REVERT: A 856 ASP cc_start: 0.8055 (t0) cc_final: 0.7709 (t0) REVERT: B 242 PHE cc_start: 0.7945 (m-80) cc_final: 0.7657 (m-80) REVERT: B 279 TYR cc_start: 0.6406 (t80) cc_final: 0.6026 (t80) REVERT: B 290 TYR cc_start: 0.6748 (m-80) cc_final: 0.5989 (m-80) REVERT: B 304 MET cc_start: 0.8550 (ptt) cc_final: 0.7736 (mmt) REVERT: B 314 MET cc_start: 0.8023 (mtt) cc_final: 0.7152 (tpp) REVERT: B 372 ASN cc_start: 0.6517 (t0) cc_final: 0.6263 (t0) REVERT: B 526 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7525 (pttt) REVERT: B 824 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7435 (tp30) REVERT: B 856 ASP cc_start: 0.7980 (t0) cc_final: 0.7596 (t0) REVERT: C 281 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5835 (tm) REVERT: C 285 MET cc_start: 0.6869 (ptm) cc_final: 0.6630 (ptt) REVERT: C 286 SER cc_start: 0.7848 (m) cc_final: 0.7380 (t) REVERT: C 304 MET cc_start: 0.6415 (ppp) cc_final: 0.5968 (mtt) REVERT: C 362 ASP cc_start: 0.8112 (t0) cc_final: 0.7875 (t0) REVERT: C 479 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 522 ASP cc_start: 0.6738 (t0) cc_final: 0.6076 (t0) REVERT: C 955 ASP cc_start: 0.6454 (m-30) cc_final: 0.6035 (p0) REVERT: C 983 SER cc_start: 0.8991 (m) cc_final: 0.8700 (p) REVERT: C 1034 ARG cc_start: 0.3187 (pmm150) cc_final: 0.2036 (ptp90) REVERT: D 281 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5510 (tm) REVERT: D 282 MET cc_start: 0.5318 (mtp) cc_final: 0.4854 (mmt) REVERT: D 286 SER cc_start: 0.7897 (m) cc_final: 0.7400 (t) REVERT: D 303 PHE cc_start: 0.7781 (m-10) cc_final: 0.7325 (m-80) REVERT: D 304 MET cc_start: 0.6607 (ppp) cc_final: 0.5925 (mtt) REVERT: D 362 ASP cc_start: 0.8084 (t0) cc_final: 0.7858 (t0) REVERT: D 479 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6943 (tm-30) REVERT: D 522 ASP cc_start: 0.6747 (t0) cc_final: 0.6084 (t0) REVERT: D 888 MET cc_start: 0.8299 (mtp) cc_final: 0.8056 (mtt) REVERT: D 955 ASP cc_start: 0.6455 (m-30) cc_final: 0.6052 (p0) REVERT: D 983 SER cc_start: 0.9013 (m) cc_final: 0.8733 (p) REVERT: D 1034 ARG cc_start: 0.3189 (pmm150) cc_final: 0.2041 (ptp90) outliers start: 59 outliers final: 47 residues processed: 328 average time/residue: 0.1462 time to fit residues: 77.3668 Evaluate side-chains 301 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 570 TYR Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 275 optimal weight: 0.7980 chunk 153 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 751 HIS ** B 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN C 874 GLN D 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110378 restraints weight = 42652.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113729 restraints weight = 23952.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115894 restraints weight = 17097.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117256 restraints weight = 13883.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118004 restraints weight = 12203.802| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23452 Z= 0.126 Angle : 0.552 9.824 31816 Z= 0.282 Chirality : 0.044 0.256 3660 Planarity : 0.003 0.042 4040 Dihedral : 5.034 64.343 3116 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.43 % Allowed : 12.09 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2884 helix: -1.19 (0.15), residues: 1076 sheet: -0.79 (0.27), residues: 394 loop : -1.17 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 342 TYR 0.013 0.001 TYR C1073 PHE 0.022 0.001 PHE C1070 TRP 0.033 0.002 TRP D 752 HIS 0.003 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00292 (23452) covalent geometry : angle 0.55249 (31816) hydrogen bonds : bond 0.03156 ( 659) hydrogen bonds : angle 4.84383 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7951 (m-80) cc_final: 0.7561 (m-10) REVERT: A 279 TYR cc_start: 0.6502 (t80) cc_final: 0.6010 (t80) REVERT: A 290 TYR cc_start: 0.6857 (m-80) cc_final: 0.6151 (m-80) REVERT: A 304 MET cc_start: 0.8495 (ptt) cc_final: 0.7735 (mmt) REVERT: A 314 MET cc_start: 0.8126 (mtt) cc_final: 0.7185 (tpp) REVERT: A 460 MET cc_start: 0.8321 (mmt) cc_final: 0.7942 (mmt) REVERT: A 526 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7497 (pttt) REVERT: A 824 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7432 (tp30) REVERT: A 856 ASP cc_start: 0.7973 (t0) cc_final: 0.7511 (t0) REVERT: B 242 PHE cc_start: 0.7952 (m-80) cc_final: 0.7565 (m-10) REVERT: B 279 TYR cc_start: 0.6560 (t80) cc_final: 0.6081 (t80) REVERT: B 290 TYR cc_start: 0.6770 (m-80) cc_final: 0.5939 (m-80) REVERT: B 304 MET cc_start: 0.8545 (ptt) cc_final: 0.7742 (mmt) REVERT: B 314 MET cc_start: 0.8014 (mtt) cc_final: 0.7083 (tpp) REVERT: B 526 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7492 (pttt) REVERT: B 856 ASP cc_start: 0.7996 (t0) cc_final: 0.7588 (t0) REVERT: C 275 TRP cc_start: 0.4684 (m-90) cc_final: 0.3684 (m100) REVERT: C 281 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5917 (tm) REVERT: C 285 MET cc_start: 0.6860 (ptm) cc_final: 0.6612 (ptt) REVERT: C 286 SER cc_start: 0.7895 (m) cc_final: 0.7412 (t) REVERT: C 304 MET cc_start: 0.6886 (ppp) cc_final: 0.5917 (mtt) REVERT: C 362 ASP cc_start: 0.8167 (t0) cc_final: 0.7947 (t0) REVERT: C 522 ASP cc_start: 0.6712 (t0) cc_final: 0.6021 (t0) REVERT: C 955 ASP cc_start: 0.6522 (m-30) cc_final: 0.6073 (p0) REVERT: C 983 SER cc_start: 0.9023 (m) cc_final: 0.8617 (p) REVERT: D 275 TRP cc_start: 0.4693 (m-90) cc_final: 0.3692 (m100) REVERT: D 281 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5323 (tm) REVERT: D 286 SER cc_start: 0.7880 (m) cc_final: 0.7389 (t) REVERT: D 304 MET cc_start: 0.6458 (ppp) cc_final: 0.5609 (mtt) REVERT: D 362 ASP cc_start: 0.8194 (t0) cc_final: 0.7958 (t0) REVERT: D 522 ASP cc_start: 0.6713 (t0) cc_final: 0.6024 (t0) REVERT: D 955 ASP cc_start: 0.6505 (m-30) cc_final: 0.6075 (p0) REVERT: D 983 SER cc_start: 0.9027 (m) cc_final: 0.8606 (p) outliers start: 62 outliers final: 47 residues processed: 309 average time/residue: 0.1633 time to fit residues: 78.6893 Evaluate side-chains 290 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1033 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1018 ARG Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1018 ARG Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 217 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 ASN D 945 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.144280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107883 restraints weight = 42832.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111117 restraints weight = 24304.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113196 restraints weight = 17493.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114485 restraints weight = 14291.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115101 restraints weight = 12624.060| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23452 Z= 0.175 Angle : 0.591 9.248 31816 Z= 0.302 Chirality : 0.045 0.270 3660 Planarity : 0.004 0.042 4040 Dihedral : 5.161 66.081 3116 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.55 % Allowed : 12.40 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.16), residues: 2884 helix: -1.13 (0.15), residues: 1080 sheet: -1.00 (0.26), residues: 408 loop : -0.98 (0.18), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.013 0.001 TYR D1073 PHE 0.023 0.002 PHE C1070 TRP 0.031 0.002 TRP D 752 HIS 0.004 0.001 HIS D 468 Details of bonding type rmsd covalent geometry : bond 0.00410 (23452) covalent geometry : angle 0.59094 (31816) hydrogen bonds : bond 0.03318 ( 659) hydrogen bonds : angle 4.92952 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7965 (m-80) cc_final: 0.7569 (m-10) REVERT: A 279 TYR cc_start: 0.6506 (t80) cc_final: 0.5962 (t80) REVERT: A 290 TYR cc_start: 0.6855 (m-80) cc_final: 0.6155 (m-80) REVERT: A 304 MET cc_start: 0.8507 (ptt) cc_final: 0.7756 (mmt) REVERT: A 314 MET cc_start: 0.8155 (mtt) cc_final: 0.7156 (tpp) REVERT: A 460 MET cc_start: 0.8345 (mmt) cc_final: 0.7920 (mmt) REVERT: A 526 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7572 (pttt) REVERT: A 824 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7545 (tp30) REVERT: A 856 ASP cc_start: 0.8053 (t0) cc_final: 0.7690 (t0) REVERT: A 1008 GLU cc_start: 0.8052 (tp30) cc_final: 0.7784 (tp30) REVERT: B 242 PHE cc_start: 0.7978 (m-80) cc_final: 0.7600 (m-10) REVERT: B 279 TYR cc_start: 0.6622 (t80) cc_final: 0.6050 (t80) REVERT: B 290 TYR cc_start: 0.6807 (m-80) cc_final: 0.5939 (m-80) REVERT: B 304 MET cc_start: 0.8579 (ptt) cc_final: 0.7745 (mmt) REVERT: B 314 MET cc_start: 0.8161 (mtt) cc_final: 0.7174 (tpp) REVERT: B 526 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7582 (pttt) REVERT: B 856 ASP cc_start: 0.8058 (t0) cc_final: 0.7688 (t0) REVERT: C 275 TRP cc_start: 0.4702 (m-90) cc_final: 0.3749 (m-10) REVERT: C 281 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5859 (tm) REVERT: C 285 MET cc_start: 0.6718 (ptm) cc_final: 0.6455 (ptt) REVERT: C 286 SER cc_start: 0.7894 (m) cc_final: 0.7412 (t) REVERT: C 304 MET cc_start: 0.7073 (ppp) cc_final: 0.6033 (mtt) REVERT: C 522 ASP cc_start: 0.6939 (t0) cc_final: 0.6693 (t70) REVERT: C 955 ASP cc_start: 0.6623 (m-30) cc_final: 0.6154 (p0) REVERT: D 275 TRP cc_start: 0.4782 (m-90) cc_final: 0.3771 (m-10) REVERT: D 285 MET cc_start: 0.6604 (ptm) cc_final: 0.6399 (ptt) REVERT: D 286 SER cc_start: 0.7865 (m) cc_final: 0.7394 (t) REVERT: D 304 MET cc_start: 0.6117 (ppp) cc_final: 0.5335 (mtt) REVERT: D 522 ASP cc_start: 0.6930 (t0) cc_final: 0.6679 (t70) REVERT: D 955 ASP cc_start: 0.6652 (m-30) cc_final: 0.6156 (p0) outliers start: 65 outliers final: 49 residues processed: 289 average time/residue: 0.1438 time to fit residues: 66.9499 Evaluate side-chains 282 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1033 CYS Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1018 ARG Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 19 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 803 ASN ** C 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.144321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108549 restraints weight = 42740.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111777 restraints weight = 27626.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112532 restraints weight = 19039.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113603 restraints weight = 16399.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113719 restraints weight = 15453.275| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23452 Z= 0.163 Angle : 0.585 8.708 31816 Z= 0.301 Chirality : 0.045 0.341 3660 Planarity : 0.004 0.042 4040 Dihedral : 5.169 64.946 3116 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 2.67 % Allowed : 12.95 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.16), residues: 2884 helix: -1.03 (0.15), residues: 1082 sheet: -1.17 (0.26), residues: 396 loop : -0.91 (0.18), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1018 TYR 0.013 0.001 TYR D1073 PHE 0.027 0.002 PHE C1070 TRP 0.033 0.002 TRP D 752 HIS 0.006 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00382 (23452) covalent geometry : angle 0.58525 (31816) hydrogen bonds : bond 0.03249 ( 659) hydrogen bonds : angle 4.90179 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7838 (m-80) cc_final: 0.7496 (m-10) REVERT: A 279 TYR cc_start: 0.6831 (t80) cc_final: 0.6276 (t80) REVERT: A 290 TYR cc_start: 0.6743 (m-80) cc_final: 0.6125 (m-80) REVERT: A 304 MET cc_start: 0.8451 (ptt) cc_final: 0.7638 (mmt) REVERT: A 314 MET cc_start: 0.8085 (mtt) cc_final: 0.7082 (tpp) REVERT: A 526 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7521 (pttt) REVERT: A 824 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7574 (tp30) REVERT: A 856 ASP cc_start: 0.8107 (t0) cc_final: 0.7786 (t0) REVERT: B 242 PHE cc_start: 0.7810 (m-80) cc_final: 0.7479 (m-10) REVERT: B 279 TYR cc_start: 0.6913 (t80) cc_final: 0.6338 (t80) REVERT: B 290 TYR cc_start: 0.6772 (m-80) cc_final: 0.6110 (m-80) REVERT: B 304 MET cc_start: 0.8505 (ptt) cc_final: 0.7565 (mmt) REVERT: B 314 MET cc_start: 0.8136 (mtt) cc_final: 0.7099 (tpp) REVERT: B 856 ASP cc_start: 0.8073 (t0) cc_final: 0.7706 (t0) REVERT: C 281 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5652 (tm) REVERT: C 282 MET cc_start: 0.5400 (mtp) cc_final: 0.4802 (mmt) REVERT: C 286 SER cc_start: 0.8062 (m) cc_final: 0.7580 (t) REVERT: C 304 MET cc_start: 0.6637 (ppp) cc_final: 0.5365 (mtt) REVERT: C 522 ASP cc_start: 0.7026 (t0) cc_final: 0.6808 (t70) REVERT: C 955 ASP cc_start: 0.6672 (m-30) cc_final: 0.6129 (p0) REVERT: C 983 SER cc_start: 0.8951 (m) cc_final: 0.8735 (p) REVERT: D 275 TRP cc_start: 0.4682 (m-90) cc_final: 0.3747 (m-10) REVERT: D 286 SER cc_start: 0.8163 (m) cc_final: 0.7749 (t) REVERT: D 304 MET cc_start: 0.6625 (ppp) cc_final: 0.5372 (mtt) REVERT: D 522 ASP cc_start: 0.6991 (t0) cc_final: 0.6777 (t70) REVERT: D 955 ASP cc_start: 0.6680 (m-30) cc_final: 0.6133 (p0) REVERT: D 983 SER cc_start: 0.8949 (m) cc_final: 0.8735 (p) outliers start: 68 outliers final: 57 residues processed: 289 average time/residue: 0.1427 time to fit residues: 66.3374 Evaluate side-chains 293 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1048 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 265 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN C 874 GLN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109728 restraints weight = 42913.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113040 restraints weight = 24076.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115200 restraints weight = 17169.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116578 restraints weight = 13933.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117212 restraints weight = 12199.929| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23452 Z= 0.117 Angle : 0.572 15.672 31816 Z= 0.288 Chirality : 0.044 0.315 3660 Planarity : 0.003 0.042 4040 Dihedral : 4.988 61.384 3116 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 2.08 % Allowed : 13.78 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.16), residues: 2884 helix: -0.94 (0.15), residues: 1110 sheet: -1.07 (0.28), residues: 368 loop : -0.90 (0.18), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1018 TYR 0.013 0.001 TYR D 318 PHE 0.022 0.001 PHE C1070 TRP 0.034 0.002 TRP D 752 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00269 (23452) covalent geometry : angle 0.57207 (31816) hydrogen bonds : bond 0.03056 ( 659) hydrogen bonds : angle 4.79415 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8088 (m-80) cc_final: 0.7741 (m-10) REVERT: A 279 TYR cc_start: 0.6790 (t80) cc_final: 0.6285 (t80) REVERT: A 290 TYR cc_start: 0.6923 (m-80) cc_final: 0.6243 (m-80) REVERT: A 304 MET cc_start: 0.8444 (ptt) cc_final: 0.7597 (mmt) REVERT: A 314 MET cc_start: 0.8235 (mtt) cc_final: 0.7207 (tpp) REVERT: A 856 ASP cc_start: 0.8054 (t0) cc_final: 0.7785 (t0) REVERT: B 242 PHE cc_start: 0.8048 (m-80) cc_final: 0.7724 (m-10) REVERT: B 279 TYR cc_start: 0.6831 (t80) cc_final: 0.6281 (t80) REVERT: B 290 TYR cc_start: 0.6996 (m-80) cc_final: 0.6221 (m-80) REVERT: B 304 MET cc_start: 0.8462 (ptt) cc_final: 0.7616 (mmt) REVERT: B 314 MET cc_start: 0.8243 (mtt) cc_final: 0.7205 (tpp) REVERT: B 856 ASP cc_start: 0.8040 (t0) cc_final: 0.7755 (t0) REVERT: C 281 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5652 (tm) REVERT: C 282 MET cc_start: 0.5551 (mtp) cc_final: 0.4945 (mmt) REVERT: C 286 SER cc_start: 0.7945 (m) cc_final: 0.7491 (t) REVERT: C 304 MET cc_start: 0.6846 (ppp) cc_final: 0.5530 (mtt) REVERT: C 522 ASP cc_start: 0.6895 (t0) cc_final: 0.6643 (t70) REVERT: C 955 ASP cc_start: 0.6555 (m-30) cc_final: 0.6103 (p0) REVERT: C 983 SER cc_start: 0.8988 (m) cc_final: 0.8708 (p) REVERT: D 275 TRP cc_start: 0.4617 (m-90) cc_final: 0.3722 (m-10) REVERT: D 286 SER cc_start: 0.7933 (m) cc_final: 0.7537 (t) REVERT: D 304 MET cc_start: 0.6448 (ppp) cc_final: 0.5172 (mtt) REVERT: D 522 ASP cc_start: 0.6901 (t0) cc_final: 0.6652 (t70) REVERT: D 955 ASP cc_start: 0.6654 (m-30) cc_final: 0.6108 (p0) REVERT: D 983 SER cc_start: 0.8974 (m) cc_final: 0.8753 (p) outliers start: 53 outliers final: 37 residues processed: 286 average time/residue: 0.1414 time to fit residues: 64.6399 Evaluate side-chains 265 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1070 PHE Chi-restraints excluded: chain D residue 246 TRP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 125 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 134 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 216 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN B 803 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.146819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110768 restraints weight = 42769.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114111 restraints weight = 24015.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116295 restraints weight = 17074.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117652 restraints weight = 13838.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118567 restraints weight = 12137.156| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23452 Z= 0.109 Angle : 0.576 14.377 31816 Z= 0.290 Chirality : 0.044 0.336 3660 Planarity : 0.004 0.055 4040 Dihedral : 4.877 58.410 3116 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.24 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.11 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2884 helix: -0.87 (0.16), residues: 1100 sheet: -1.01 (0.28), residues: 368 loop : -0.87 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 342 TYR 0.012 0.001 TYR C 318 PHE 0.050 0.001 PHE B 804 TRP 0.045 0.002 TRP D 246 HIS 0.009 0.001 HIS B 805 Details of bonding type rmsd covalent geometry : bond 0.00246 (23452) covalent geometry : angle 0.57574 (31816) hydrogen bonds : bond 0.02945 ( 659) hydrogen bonds : angle 4.75533 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.8126 (m-80) cc_final: 0.7832 (m-10) REVERT: A 279 TYR cc_start: 0.6795 (t80) cc_final: 0.6308 (t80) REVERT: A 290 TYR cc_start: 0.6977 (m-80) cc_final: 0.6303 (m-80) REVERT: A 304 MET cc_start: 0.8452 (ptt) cc_final: 0.7609 (mmt) REVERT: A 314 MET cc_start: 0.8257 (mtt) cc_final: 0.7239 (tpp) REVERT: A 506 MET cc_start: 0.8037 (tpp) cc_final: 0.7492 (tpp) REVERT: A 856 ASP cc_start: 0.8049 (t0) cc_final: 0.7799 (t0) REVERT: B 242 PHE cc_start: 0.8088 (m-80) cc_final: 0.7803 (m-10) REVERT: B 279 TYR cc_start: 0.6737 (t80) cc_final: 0.6221 (t80) REVERT: B 290 TYR cc_start: 0.7035 (m-80) cc_final: 0.6302 (m-80) REVERT: B 304 MET cc_start: 0.8451 (ptt) cc_final: 0.7587 (mmt) REVERT: B 314 MET cc_start: 0.8175 (mtt) cc_final: 0.7175 (tpp) REVERT: B 803 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7481 (t0) REVERT: B 856 ASP cc_start: 0.8044 (t0) cc_final: 0.7804 (t0) REVERT: C 281 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5641 (tm) REVERT: C 282 MET cc_start: 0.5593 (mtp) cc_final: 0.5017 (mmt) REVERT: C 286 SER cc_start: 0.7925 (m) cc_final: 0.7488 (t) REVERT: C 304 MET cc_start: 0.6714 (ppp) cc_final: 0.5380 (mtt) REVERT: C 479 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 522 ASP cc_start: 0.6800 (t0) cc_final: 0.6537 (t70) REVERT: C 955 ASP cc_start: 0.6504 (m-30) cc_final: 0.6091 (p0) REVERT: C 983 SER cc_start: 0.8964 (m) cc_final: 0.8697 (p) REVERT: D 275 TRP cc_start: 0.4635 (m-90) cc_final: 0.3777 (m-10) REVERT: D 286 SER cc_start: 0.7936 (m) cc_final: 0.7511 (t) REVERT: D 304 MET cc_start: 0.6541 (ppp) cc_final: 0.5340 (mtt) REVERT: D 479 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7304 (tm-30) REVERT: D 522 ASP cc_start: 0.6802 (t0) cc_final: 0.6539 (t70) REVERT: D 955 ASP cc_start: 0.6525 (m-30) cc_final: 0.6101 (p0) REVERT: D 983 SER cc_start: 0.8972 (m) cc_final: 0.8709 (p) outliers start: 45 outliers final: 36 residues processed: 261 average time/residue: 0.1481 time to fit residues: 62.4514 Evaluate side-chains 255 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 365 HIS Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 982 MET Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain D residue 246 TRP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 365 HIS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1070 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 66 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107899 restraints weight = 42952.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113669 restraints weight = 25845.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113443 restraints weight = 15226.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113895 restraints weight = 14595.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113960 restraints weight = 13585.469| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23452 Z= 0.167 Angle : 0.613 13.874 31816 Z= 0.308 Chirality : 0.046 0.336 3660 Planarity : 0.004 0.042 4040 Dihedral : 5.045 60.283 3116 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 1.81 % Allowed : 14.44 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.16), residues: 2884 helix: -0.80 (0.16), residues: 1080 sheet: -1.08 (0.28), residues: 370 loop : -0.84 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1018 TYR 0.020 0.001 TYR D 318 PHE 0.040 0.002 PHE D1070 TRP 0.030 0.002 TRP C 752 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00393 (23452) covalent geometry : angle 0.61311 (31816) hydrogen bonds : bond 0.03114 ( 659) hydrogen bonds : angle 4.83475 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3722.26 seconds wall clock time: 65 minutes 11.68 seconds (3911.68 seconds total)