Starting phenix.real_space_refine on Fri Mar 6 08:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk4_32558/03_2026/7wk4_32558.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk4_32558/03_2026/7wk4_32558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wk4_32558/03_2026/7wk4_32558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk4_32558/03_2026/7wk4_32558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk4_32558/03_2026/7wk4_32558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk4_32558/03_2026/7wk4_32558.map" } resolution = 3.69 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= 0.006 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18904 2.51 5 N 4917 2.21 5 O 5577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 29541 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4736 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 27, 'TRANS': 553} Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Time building chain proxies: 6.47, per 1000 atoms: 0.22 Number of scatterers: 29541 At special positions: 0 Unit cell: (151.927, 138.811, 233.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5577 8.00 N 4917 7.00 C 18904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.04 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 25.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.658A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.835A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.525A pdb=" N GLN A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.863A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.646A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 4.069A pdb=" N ASN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.519A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.596A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.804A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.077A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 220 through 248 removed outlier: 4.246A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.658A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.977A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.797A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.503A pdb=" N VAL A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 removed outlier: 3.822A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.524A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.545A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.000A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.572A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 removed outlier: 4.155A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.512A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.968A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.805A pdb=" N ILE A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.697A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 515 through 530 removed outlier: 4.134A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.948A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.645A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.719A pdb=" N LYS B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.804A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.719A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.524A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.945A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.517A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.720A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.533A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.511A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.607A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.667A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.762A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.843A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.556A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.510A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.516A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.649A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.604A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.530A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.619A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.541A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.537A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.576A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.740A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.832A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.907A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.959A pdb=" N TYR D 421 " --> pdb=" O ASN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 639 removed outlier: 3.977A pdb=" N SER D 637 " --> pdb=" O ARG D 634 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR D 638 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY D 639 " --> pdb=" O TYR D 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 639' Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.533A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.966A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 746 through 751' Processing helix chain 'D' and resid 759 through 770 removed outlier: 3.688A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 783 removed outlier: 3.909A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 824 removed outlier: 4.095A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.637A pdb=" N THR D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.720A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.925A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 918' Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.739A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 965 " --> pdb=" O THR D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 3.937A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 993 " --> pdb=" O ALA D 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.689A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.804A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.577A pdb=" N THR B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.704A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.658A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.444A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.549A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.724A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 402 removed outlier: 3.659A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.637A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.412A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.206A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.816A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.882A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.886A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.596A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.979A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.998A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.444A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.689A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.845A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.845A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.231A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.469A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.692A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.539A pdb=" N HIS D 49 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.912A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 317 removed outlier: 3.735A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 325 through 328 removed outlier: 3.620A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 548 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.593A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 511 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.520A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 660 removed outlier: 4.959A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 666 " --> pdb=" O ILE D 670 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.664A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.604A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1094 through 1097 removed outlier: 3.632A pdb=" N VAL D1104 " --> pdb=" O GLN D1113 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.91 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5779 1.33 - 1.46: 10962 1.46 - 1.60: 13319 1.60 - 1.73: 0 1.73 - 1.86: 194 Bond restraints: 30254 Sorted by residual: bond pdb=" CA THR C 581 " pdb=" C THR C 581 " ideal model delta sigma weight residual 1.533 1.466 0.068 5.60e-03 3.19e+04 1.45e+02 bond pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.27e-02 6.20e+03 7.32e+01 bond pdb=" CA TYR D 380 " pdb=" C TYR D 380 " ideal model delta sigma weight residual 1.523 1.428 0.096 1.34e-02 5.57e+03 5.08e+01 bond pdb=" N ILE C 584 " pdb=" CA ILE C 584 " ideal model delta sigma weight residual 1.459 1.379 0.080 1.15e-02 7.56e+03 4.82e+01 bond pdb=" N ILE D 980 " pdb=" CA ILE D 980 " ideal model delta sigma weight residual 1.461 1.386 0.075 1.17e-02 7.31e+03 4.10e+01 ... (remaining 30249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 40196 2.50 - 5.01: 831 5.01 - 7.51: 77 7.51 - 10.02: 26 10.02 - 12.52: 4 Bond angle restraints: 41134 Sorted by residual: angle pdb=" CA ASP C 578 " pdb=" C ASP C 578 " pdb=" N PRO C 579 " ideal model delta sigma weight residual 119.27 110.11 9.16 1.13e+00 7.83e-01 6.57e+01 angle pdb=" N ALA B 989 " pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.24e+01 angle pdb=" C THR C 581 " pdb=" CA THR C 581 " pdb=" CB THR C 581 " ideal model delta sigma weight residual 117.07 106.24 10.83 1.44e+00 4.82e-01 5.65e+01 angle pdb=" N ILE D 980 " pdb=" CA ILE D 980 " pdb=" C ILE D 980 " ideal model delta sigma weight residual 110.42 103.77 6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" N PHE D 981 " pdb=" CA PHE D 981 " pdb=" C PHE D 981 " ideal model delta sigma weight residual 111.28 118.78 -7.50 1.09e+00 8.42e-01 4.74e+01 ... (remaining 41129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16048 17.95 - 35.91: 1586 35.91 - 53.86: 306 53.86 - 71.81: 69 71.81 - 89.77: 26 Dihedral angle restraints: 18035 sinusoidal: 7115 harmonic: 10920 Sorted by residual: dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.42 -80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual 93.00 169.16 -76.16 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -20.80 -65.20 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 18032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4077 0.088 - 0.176: 452 0.176 - 0.264: 55 0.264 - 0.351: 9 0.351 - 0.439: 1 Chirality restraints: 4594 Sorted by residual: chirality pdb=" CA PHE D 981 " pdb=" N PHE D 981 " pdb=" C PHE D 981 " pdb=" CB PHE D 981 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA SER D 982 " pdb=" N SER D 982 " pdb=" C SER D 982 " pdb=" CB SER D 982 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLU B 990 " pdb=" N GLU B 990 " pdb=" C GLU B 990 " pdb=" CB GLU B 990 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4591 not shown) Planarity restraints: 5319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 578 " -0.027 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C ASP C 578 " 0.101 2.00e-02 2.50e+03 pdb=" O ASP C 578 " -0.040 2.00e-02 2.50e+03 pdb=" N PRO C 579 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO D 987 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.066 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO C 987 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.056 5.00e-02 4.00e+02 ... (remaining 5316 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10080 2.85 - 3.36: 22721 3.36 - 3.88: 48642 3.88 - 4.39: 52644 4.39 - 4.90: 91942 Nonbonded interactions: 226029 Sorted by model distance: nonbonded pdb=" O GLN B 957 " pdb=" OG1 THR B 961 " model vdw 2.338 3.040 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.341 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.352 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.356 3.040 nonbonded pdb=" O ASP D 290 " pdb=" OG SER D 297 " model vdw 2.357 3.040 ... (remaining 226024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'D' and (resid 14 through 631 or resid 641 through 1147)) } 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.850 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 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 : 0.005 0.109 30296 Z= 0.295 Angle : 0.862 12.523 41218 Z= 0.514 Chirality : 0.055 0.439 4594 Planarity : 0.007 0.109 5319 Dihedral : 14.662 89.768 10875 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 0.49 % Allowed : 8.50 % Favored : 91.01 % Cbeta Deviations : 0.06 % 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: -4.28 (0.10), residues: 3693 helix: -5.04 (0.04), residues: 853 sheet: -1.22 (0.18), residues: 641 loop : -2.49 (0.10), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.021 0.001 TYR A 385 PHE 0.034 0.001 PHE B 377 TRP 0.014 0.001 TRP A 275 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00511 (30254) covalent geometry : angle 0.86015 (41134) SS BOND : bond 0.00596 ( 42) SS BOND : angle 1.48214 ( 84) hydrogen bonds : bond 0.30909 ( 875) hydrogen bonds : angle 11.19840 ( 2466) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 605 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: -0.0669 (tmm) cc_final: -0.0909 (tmm) REVERT: A 383 MET cc_start: 0.3120 (mtp) cc_final: 0.2324 (tpp) REVERT: B 40 ASP cc_start: 0.8699 (p0) cc_final: 0.8476 (p0) REVERT: B 308 VAL cc_start: 0.8421 (t) cc_final: 0.8101 (t) REVERT: B 921 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6922 (tttp) REVERT: B 970 PHE cc_start: 0.8374 (m-80) cc_final: 0.7811 (m-80) REVERT: B 1139 ASP cc_start: 0.7026 (t0) cc_final: 0.6726 (p0) REVERT: C 351 TYR cc_start: 0.7649 (p90) cc_final: 0.7311 (p90) REVERT: C 377 PHE cc_start: 0.4885 (p90) cc_final: 0.4309 (p90) REVERT: C 740 MET cc_start: 0.7370 (tpt) cc_final: 0.6988 (tpp) REVERT: D 153 MET cc_start: -0.2134 (ttp) cc_final: -0.2864 (mtm) REVERT: D 436 TRP cc_start: 0.3595 (t60) cc_final: 0.3128 (t-100) REVERT: D 452 LEU cc_start: 0.5650 (mt) cc_final: 0.5321 (mt) REVERT: D 710 ASN cc_start: 0.6396 (p0) cc_final: 0.6144 (p0) REVERT: D 752 LEU cc_start: 0.7923 (mt) cc_final: 0.7671 (mp) REVERT: D 898 PHE cc_start: 0.5868 (m-10) cc_final: 0.5599 (m-80) REVERT: D 950 ASP cc_start: 0.6489 (p0) cc_final: 0.6185 (p0) outliers start: 16 outliers final: 6 residues processed: 619 average time/residue: 0.1807 time to fit residues: 179.9632 Evaluate side-chains 373 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 367 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 9.9990 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 241 HIS A 340 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN B 437 ASN B 487 ASN B 542 ASN B 641 ASN B 824 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 134 GLN C 394 ASN C 448 ASN C 505 HIS C 563 GLN C 717 ASN C 787 GLN C 901 GLN C 914 ASN C 935 GLN C 955 ASN C 960 ASN C 992 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 66 HIS D 239 GLN D 394 ASN D 505 HIS D 690 GLN D 751 ASN D 777 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D 914 ASN D 925 ASN D 926 GLN D 935 GLN D 957 GLN D1135 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.152102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.124896 restraints weight = 114366.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.126710 restraints weight = 68818.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.127658 restraints weight = 47230.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.128010 restraints weight = 38125.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.128196 restraints weight = 31430.771| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30296 Z= 0.119 Angle : 0.586 12.278 41218 Z= 0.306 Chirality : 0.043 0.181 4594 Planarity : 0.005 0.070 5319 Dihedral : 4.374 52.193 4023 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 14.47 % Favored : 83.61 % 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: -2.92 (0.11), residues: 3693 helix: -2.83 (0.12), residues: 890 sheet: -0.37 (0.19), residues: 583 loop : -2.05 (0.11), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.022 0.001 TYR D 380 PHE 0.025 0.001 PHE C 55 TRP 0.020 0.001 TRP C 886 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00254 (30254) covalent geometry : angle 0.58340 (41134) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.42230 ( 84) hydrogen bonds : bond 0.04999 ( 875) hydrogen bonds : angle 6.39054 ( 2466) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 402 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.0133 (tmm) cc_final: -0.0100 (tmm) REVERT: A 245 ARG cc_start: 0.1031 (ttm170) cc_final: 0.0827 (mmm-85) REVERT: A 340 GLN cc_start: 0.2931 (OUTLIER) cc_final: 0.2720 (tp40) REVERT: A 554 LEU cc_start: -0.0515 (tp) cc_final: -0.0970 (pp) REVERT: B 201 PHE cc_start: 0.6337 (m-80) cc_final: 0.5923 (t80) REVERT: B 308 VAL cc_start: 0.8392 (t) cc_final: 0.8136 (t) REVERT: B 970 PHE cc_start: 0.8603 (m-80) cc_final: 0.7968 (m-80) REVERT: B 1088 HIS cc_start: 0.6451 (OUTLIER) cc_final: 0.5857 (t-90) REVERT: B 1139 ASP cc_start: 0.7421 (t0) cc_final: 0.6688 (p0) REVERT: C 377 PHE cc_start: 0.4899 (p90) cc_final: 0.4297 (p90) REVERT: C 740 MET cc_start: 0.7803 (tpt) cc_final: 0.7237 (tpp) REVERT: D 153 MET cc_start: -0.2651 (ttp) cc_final: -0.3190 (mtm) REVERT: D 202 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8274 (tptt) REVERT: D 436 TRP cc_start: 0.3193 (t60) cc_final: 0.2948 (t-100) REVERT: D 710 ASN cc_start: 0.6907 (p0) cc_final: 0.6547 (p0) REVERT: D 725 GLU cc_start: 0.7150 (tt0) cc_final: 0.6940 (tt0) REVERT: D 898 PHE cc_start: 0.6596 (m-10) cc_final: 0.6386 (m-80) REVERT: D 965 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7672 (tp-100) outliers start: 63 outliers final: 32 residues processed: 438 average time/residue: 0.1687 time to fit residues: 122.2524 Evaluate side-chains 360 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 326 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1049 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 78 optimal weight: 6.9990 chunk 292 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 341 optimal weight: 3.9990 chunk 301 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 949 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C 777 ASN C 957 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN D 61 ASN ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN D1036 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.148368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.120447 restraints weight = 113185.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.121853 restraints weight = 72610.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.122257 restraints weight = 46868.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.122716 restraints weight = 39277.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.122814 restraints weight = 35391.683| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 30296 Z= 0.140 Angle : 0.562 11.674 41218 Z= 0.291 Chirality : 0.043 0.187 4594 Planarity : 0.004 0.056 5319 Dihedral : 4.151 33.896 4022 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.96 % Allowed : 15.17 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.98 (0.12), residues: 3693 helix: -1.23 (0.16), residues: 891 sheet: -0.14 (0.20), residues: 589 loop : -1.73 (0.11), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 905 TYR 0.018 0.001 TYR B 707 PHE 0.023 0.002 PHE B 817 TRP 0.024 0.001 TRP C 886 HIS 0.022 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00299 (30254) covalent geometry : angle 0.55783 (41134) SS BOND : bond 0.01057 ( 42) SS BOND : angle 1.60996 ( 84) hydrogen bonds : bond 0.03928 ( 875) hydrogen bonds : angle 5.66359 ( 2466) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 347 time to evaluate : 1.101 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: A 190 MET cc_start: 0.0358 (tmm) cc_final: -0.0270 (tmm) REVERT: A 340 GLN cc_start: 0.2178 (OUTLIER) cc_final: 0.1969 (tp40) REVERT: A 554 LEU cc_start: -0.1056 (tp) cc_final: -0.1641 (pp) REVERT: B 301 CYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7189 (t) REVERT: B 308 VAL cc_start: 0.8536 (t) cc_final: 0.8329 (t) REVERT: B 868 GLU cc_start: 0.7620 (mp0) cc_final: 0.7258 (tm-30) REVERT: B 978 ASN cc_start: 0.7668 (p0) cc_final: 0.6918 (p0) REVERT: B 988 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7703 (mp0) REVERT: B 1139 ASP cc_start: 0.7375 (t0) cc_final: 0.6593 (p0) REVERT: C 377 PHE cc_start: 0.5288 (p90) cc_final: 0.4704 (p90) REVERT: C 480 CYS cc_start: 0.1444 (OUTLIER) cc_final: 0.0429 (t) REVERT: C 636 TYR cc_start: 0.6508 (m-80) cc_final: 0.6299 (m-80) REVERT: C 740 MET cc_start: 0.7760 (tpt) cc_final: 0.7400 (tpp) REVERT: C 1050 MET cc_start: 0.6979 (ptp) cc_final: 0.6640 (ptp) REVERT: D 90 VAL cc_start: 0.8636 (t) cc_final: 0.8375 (m) REVERT: D 153 MET cc_start: -0.2532 (ttp) cc_final: -0.3212 (mtm) REVERT: D 436 TRP cc_start: 0.3193 (t60) cc_final: 0.2987 (t-100) REVERT: D 710 ASN cc_start: 0.6998 (p0) cc_final: 0.6611 (p0) REVERT: D 725 GLU cc_start: 0.7280 (tt0) cc_final: 0.7030 (tt0) REVERT: D 767 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7353 (mm) REVERT: D 965 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7853 (tp-100) outliers start: 97 outliers final: 53 residues processed: 411 average time/residue: 0.1631 time to fit residues: 112.6001 Evaluate side-chains 353 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 296 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 258 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 278 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C1002 GLN D 935 GLN D1005 GLN D1011 GLN ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.147602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119896 restraints weight = 112349.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.121015 restraints weight = 74649.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.121362 restraints weight = 46633.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.121622 restraints weight = 44595.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.121741 restraints weight = 40098.745| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30296 Z= 0.119 Angle : 0.547 11.626 41218 Z= 0.279 Chirality : 0.043 0.204 4594 Planarity : 0.004 0.048 5319 Dihedral : 4.083 31.709 4020 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.83 % Allowed : 16.61 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.49 (0.13), residues: 3693 helix: -0.48 (0.17), residues: 893 sheet: 0.11 (0.20), residues: 568 loop : -1.55 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 245 TYR 0.021 0.001 TYR D1007 PHE 0.035 0.001 PHE C1121 TRP 0.024 0.001 TRP C 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00267 (30254) covalent geometry : angle 0.54222 (41134) SS BOND : bond 0.00593 ( 42) SS BOND : angle 1.64231 ( 84) hydrogen bonds : bond 0.03535 ( 875) hydrogen bonds : angle 5.30384 ( 2466) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 343 time to evaluate : 1.114 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: A 190 MET cc_start: -0.0009 (tmm) cc_final: -0.0645 (tmm) REVERT: A 245 ARG cc_start: 0.0499 (ttm170) cc_final: -0.0062 (tpp-160) REVERT: A 266 LEU cc_start: 0.0141 (OUTLIER) cc_final: -0.0224 (pp) REVERT: B 301 CYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7336 (t) REVERT: B 725 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7524 (tm-30) REVERT: B 988 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7857 (mp0) REVERT: B 1139 ASP cc_start: 0.7382 (t0) cc_final: 0.6654 (p0) REVERT: C 351 TYR cc_start: 0.7586 (p90) cc_final: 0.7334 (p90) REVERT: C 377 PHE cc_start: 0.5334 (p90) cc_final: 0.4745 (p90) REVERT: C 480 CYS cc_start: 0.1563 (OUTLIER) cc_final: 0.0585 (t) REVERT: C 582 LEU cc_start: 0.8457 (tp) cc_final: 0.8124 (pt) REVERT: C 740 MET cc_start: 0.7707 (tpt) cc_final: 0.7309 (tpp) REVERT: C 1050 MET cc_start: 0.6797 (ptp) cc_final: 0.6474 (ptp) REVERT: D 90 VAL cc_start: 0.8681 (t) cc_final: 0.8429 (m) REVERT: D 153 MET cc_start: -0.2350 (ttp) cc_final: -0.2904 (mtm) REVERT: D 436 TRP cc_start: 0.3315 (t60) cc_final: 0.3087 (t-100) REVERT: D 664 ILE cc_start: 0.8010 (mt) cc_final: 0.7729 (tt) REVERT: D 710 ASN cc_start: 0.7190 (p0) cc_final: 0.6883 (p0) REVERT: D 725 GLU cc_start: 0.7376 (tt0) cc_final: 0.7123 (tt0) REVERT: D 917 TYR cc_start: 0.6803 (m-80) cc_final: 0.6397 (m-80) REVERT: D 965 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7932 (tp-100) outliers start: 93 outliers final: 60 residues processed: 406 average time/residue: 0.1686 time to fit residues: 114.8724 Evaluate side-chains 367 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 96 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 303 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 327 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 115 GLN B 245 HIS B 271 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 955 ASN C1002 GLN D 703 ASN D1005 GLN D1010 GLN ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.144591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.115415 restraints weight = 111350.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.117322 restraints weight = 71316.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.117632 restraints weight = 44843.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.118063 restraints weight = 36664.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.118131 restraints weight = 34639.117| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 30296 Z= 0.169 Angle : 0.602 11.684 41218 Z= 0.307 Chirality : 0.045 0.234 4594 Planarity : 0.004 0.048 5319 Dihedral : 4.290 34.657 4020 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.72 % Allowed : 17.61 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.38 (0.13), residues: 3693 helix: -0.25 (0.17), residues: 887 sheet: -0.16 (0.19), residues: 623 loop : -1.46 (0.12), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 905 TYR 0.023 0.002 TYR B 91 PHE 0.023 0.002 PHE C1121 TRP 0.016 0.001 TRP C 886 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00387 (30254) covalent geometry : angle 0.59713 (41134) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.74038 ( 84) hydrogen bonds : bond 0.03728 ( 875) hydrogen bonds : angle 5.35393 ( 2466) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 328 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0013 (OUTLIER) cc_final: -0.0370 (pp) REVERT: A 302 TRP cc_start: 0.2155 (OUTLIER) cc_final: -0.0507 (m100) REVERT: B 301 CYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7583 (t) REVERT: B 725 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 868 GLU cc_start: 0.7913 (mp0) cc_final: 0.7365 (tm-30) REVERT: B 960 ASN cc_start: 0.8505 (p0) cc_final: 0.7487 (p0) REVERT: B 988 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7881 (mp0) REVERT: B 1139 ASP cc_start: 0.7326 (t0) cc_final: 0.6612 (p0) REVERT: C 271 GLN cc_start: 0.7504 (mm-40) cc_final: 0.6986 (tm-30) REVERT: C 351 TYR cc_start: 0.7816 (p90) cc_final: 0.7608 (p90) REVERT: C 480 CYS cc_start: 0.0932 (OUTLIER) cc_final: -0.0091 (t) REVERT: C 951 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 954 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.6304 (m-70) REVERT: C 1002 GLN cc_start: 0.7289 (mt0) cc_final: 0.7087 (mt0) REVERT: C 1050 MET cc_start: 0.6904 (ptp) cc_final: 0.6490 (ptp) REVERT: D 90 VAL cc_start: 0.8776 (t) cc_final: 0.8538 (m) REVERT: D 153 MET cc_start: -0.2440 (ttp) cc_final: -0.2817 (mtm) REVERT: D 436 TRP cc_start: 0.3428 (t60) cc_final: 0.3227 (t-100) REVERT: D 710 ASN cc_start: 0.7284 (p0) cc_final: 0.6898 (p0) REVERT: D 725 GLU cc_start: 0.7405 (tt0) cc_final: 0.7105 (tt0) REVERT: D 767 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7547 (mm) REVERT: D 917 TYR cc_start: 0.7059 (m-80) cc_final: 0.6494 (m-80) REVERT: D 965 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8126 (tp-100) outliers start: 122 outliers final: 80 residues processed: 410 average time/residue: 0.1638 time to fit residues: 113.2912 Evaluate side-chains 383 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 353 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 114 optimal weight: 0.0170 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.0370 chunk 111 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1108 ASN D 519 HIS D 935 GLN D 955 ASN D1005 GLN ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.146081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.117099 restraints weight = 112136.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.119206 restraints weight = 70880.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.119286 restraints weight = 43475.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.119898 restraints weight = 38732.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120046 restraints weight = 33183.629| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 30296 Z= 0.099 Angle : 0.551 11.708 41218 Z= 0.276 Chirality : 0.044 0.196 4594 Planarity : 0.004 0.048 5319 Dihedral : 4.039 34.418 4018 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.59 % Allowed : 19.13 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.20 (0.13), residues: 3693 helix: -0.05 (0.17), residues: 897 sheet: -0.13 (0.19), residues: 620 loop : -1.35 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 245 TYR 0.024 0.001 TYR D1007 PHE 0.019 0.001 PHE B 817 TRP 0.016 0.001 TRP C 886 HIS 0.011 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00221 (30254) covalent geometry : angle 0.54838 (41134) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.39888 ( 84) hydrogen bonds : bond 0.03290 ( 875) hydrogen bonds : angle 5.12141 ( 2466) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 334 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0083 (OUTLIER) cc_final: -0.0283 (pp) REVERT: A 302 TRP cc_start: 0.1948 (OUTLIER) cc_final: -0.0618 (m100) REVERT: B 121 ASN cc_start: 0.1553 (OUTLIER) cc_final: 0.0241 (m-40) REVERT: B 301 CYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7546 (t) REVERT: B 567 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7409 (ttm-80) REVERT: B 725 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 868 GLU cc_start: 0.7989 (mp0) cc_final: 0.7408 (tm-30) REVERT: B 960 ASN cc_start: 0.8430 (p0) cc_final: 0.7640 (p0) REVERT: B 988 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7818 (mp0) REVERT: B 1139 ASP cc_start: 0.7401 (t0) cc_final: 0.6698 (p0) REVERT: C 271 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7031 (tm-30) REVERT: C 480 CYS cc_start: 0.0956 (OUTLIER) cc_final: -0.0059 (t) REVERT: C 951 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8604 (p) REVERT: C 954 HIS cc_start: 0.6876 (OUTLIER) cc_final: 0.6452 (m-70) REVERT: C 1050 MET cc_start: 0.6731 (ptp) cc_final: 0.6354 (ptp) REVERT: D 90 VAL cc_start: 0.8786 (t) cc_final: 0.8548 (m) REVERT: D 153 MET cc_start: -0.2667 (ttp) cc_final: -0.2917 (mtm) REVERT: D 436 TRP cc_start: 0.3702 (t60) cc_final: 0.3444 (t-100) REVERT: D 697 MET cc_start: 0.7450 (ppp) cc_final: 0.7050 (ppp) REVERT: D 710 ASN cc_start: 0.7405 (p0) cc_final: 0.7016 (p0) REVERT: D 725 GLU cc_start: 0.7369 (tt0) cc_final: 0.7079 (tt0) REVERT: D 965 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8045 (tp-100) outliers start: 85 outliers final: 62 residues processed: 390 average time/residue: 0.1633 time to fit residues: 107.0274 Evaluate side-chains 370 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 233 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 328 optimal weight: 0.3980 chunk 199 optimal weight: 1.9990 chunk 249 optimal weight: 0.0270 chunk 82 optimal weight: 6.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 519 HIS D 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.145910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.117478 restraints weight = 112682.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.119342 restraints weight = 66084.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.119229 restraints weight = 43818.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.120060 restraints weight = 36293.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.119972 restraints weight = 29454.854| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 30296 Z= 0.104 Angle : 0.552 11.057 41218 Z= 0.275 Chirality : 0.043 0.192 4594 Planarity : 0.003 0.047 5319 Dihedral : 3.982 34.761 4018 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.74 % Allowed : 19.56 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.08 (0.13), residues: 3693 helix: 0.11 (0.18), residues: 888 sheet: -0.06 (0.20), residues: 605 loop : -1.29 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 245 TYR 0.025 0.001 TYR D 917 PHE 0.027 0.001 PHE D 201 TRP 0.012 0.001 TRP C 886 HIS 0.021 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00236 (30254) covalent geometry : angle 0.54947 (41134) SS BOND : bond 0.00346 ( 42) SS BOND : angle 1.27821 ( 84) hydrogen bonds : bond 0.03251 ( 875) hydrogen bonds : angle 5.02104 ( 2466) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 319 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0176 (OUTLIER) cc_final: -0.0501 (pp) REVERT: A 302 TRP cc_start: 0.2247 (OUTLIER) cc_final: -0.0361 (m100) REVERT: B 301 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (t) REVERT: B 567 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7472 (ttm-80) REVERT: B 725 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 960 ASN cc_start: 0.8437 (p0) cc_final: 0.7786 (p0) REVERT: B 988 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7827 (mp0) REVERT: B 1139 ASP cc_start: 0.7348 (t0) cc_final: 0.6666 (p0) REVERT: C 271 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7063 (tm-30) REVERT: C 400 PHE cc_start: 0.3339 (OUTLIER) cc_final: 0.2153 (p90) REVERT: C 480 CYS cc_start: 0.1226 (OUTLIER) cc_final: 0.0152 (t) REVERT: C 951 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 954 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6531 (m-70) REVERT: C 1002 GLN cc_start: 0.7569 (mt0) cc_final: 0.7354 (mt0) REVERT: C 1050 MET cc_start: 0.6698 (ptp) cc_final: 0.6267 (ptp) REVERT: C 1120 THR cc_start: 0.7488 (p) cc_final: 0.7170 (t) REVERT: D 90 VAL cc_start: 0.8803 (t) cc_final: 0.8565 (m) REVERT: D 153 MET cc_start: -0.2721 (ttp) cc_final: -0.3049 (mtm) REVERT: D 177 MET cc_start: -0.1895 (mmt) cc_final: -0.2846 (mmm) REVERT: D 436 TRP cc_start: 0.3811 (t60) cc_final: 0.3531 (t-100) REVERT: D 501 TYR cc_start: 0.4858 (OUTLIER) cc_final: 0.4085 (m-80) REVERT: D 697 MET cc_start: 0.7586 (ppp) cc_final: 0.7265 (ppp) REVERT: D 710 ASN cc_start: 0.7552 (p0) cc_final: 0.7108 (p0) REVERT: D 725 GLU cc_start: 0.7463 (tt0) cc_final: 0.7100 (tt0) REVERT: D 864 LEU cc_start: 0.8535 (tt) cc_final: 0.8028 (tp) REVERT: D 965 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8076 (tp-100) REVERT: D 1017 GLU cc_start: 0.7684 (tp30) cc_final: 0.7476 (tp30) outliers start: 90 outliers final: 66 residues processed: 377 average time/residue: 0.1631 time to fit residues: 103.8012 Evaluate side-chains 370 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 296 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 222 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 314 optimal weight: 8.9990 chunk 203 optimal weight: 0.0970 chunk 356 optimal weight: 8.9990 chunk 295 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.115860 restraints weight = 112809.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.117081 restraints weight = 75579.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.117613 restraints weight = 50893.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.117993 restraints weight = 42204.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.118148 restraints weight = 38025.672| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30296 Z= 0.121 Angle : 0.574 11.452 41218 Z= 0.287 Chirality : 0.044 0.187 4594 Planarity : 0.004 0.048 5319 Dihedral : 4.029 35.022 4018 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.71 % Allowed : 19.90 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 3693 helix: 0.19 (0.18), residues: 883 sheet: 0.01 (0.19), residues: 625 loop : -1.23 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 983 TYR 0.026 0.001 TYR D1007 PHE 0.022 0.001 PHE D 201 TRP 0.011 0.001 TRP C 886 HIS 0.040 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00274 (30254) covalent geometry : angle 0.57091 (41134) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.36448 ( 84) hydrogen bonds : bond 0.03331 ( 875) hydrogen bonds : angle 5.03822 ( 2466) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 314 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0240 (OUTLIER) cc_final: -0.0504 (pp) REVERT: A 302 TRP cc_start: 0.2016 (OUTLIER) cc_final: -0.0676 (m100) REVERT: B 189 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7353 (mt) REVERT: B 301 CYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7663 (t) REVERT: B 567 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7508 (ttm-80) REVERT: B 697 MET cc_start: 0.7888 (mtp) cc_final: 0.7438 (ttm) REVERT: B 725 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 818 ILE cc_start: 0.8468 (pt) cc_final: 0.7997 (mt) REVERT: B 868 GLU cc_start: 0.7986 (pm20) cc_final: 0.7622 (tm-30) REVERT: B 960 ASN cc_start: 0.8153 (p0) cc_final: 0.7952 (p0) REVERT: B 988 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7854 (mp0) REVERT: B 1139 ASP cc_start: 0.7158 (t0) cc_final: 0.6597 (p0) REVERT: C 400 PHE cc_start: 0.3494 (OUTLIER) cc_final: 0.2319 (p90) REVERT: C 480 CYS cc_start: 0.0992 (OUTLIER) cc_final: -0.0203 (t) REVERT: C 951 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (p) REVERT: C 954 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.6408 (m-70) REVERT: C 1050 MET cc_start: 0.6842 (ptp) cc_final: 0.6561 (ptm) REVERT: D 90 VAL cc_start: 0.8808 (t) cc_final: 0.8576 (m) REVERT: D 153 MET cc_start: -0.2812 (ttp) cc_final: -0.3164 (mtm) REVERT: D 177 MET cc_start: -0.1946 (mmt) cc_final: -0.2884 (mmm) REVERT: D 436 TRP cc_start: 0.3619 (t60) cc_final: 0.3414 (t-100) REVERT: D 501 TYR cc_start: 0.5249 (OUTLIER) cc_final: 0.4239 (m-80) REVERT: D 725 GLU cc_start: 0.7296 (tt0) cc_final: 0.7003 (tt0) REVERT: D 965 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8048 (tp-100) REVERT: D 1017 GLU cc_start: 0.7470 (tp30) cc_final: 0.7220 (tp30) outliers start: 89 outliers final: 74 residues processed: 372 average time/residue: 0.1634 time to fit residues: 102.3058 Evaluate side-chains 375 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 292 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 241 optimal weight: 1.9990 chunk 345 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 344 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 519 HIS D 710 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.144585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.116049 restraints weight = 111882.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.117349 restraints weight = 70587.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.118021 restraints weight = 45307.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.118270 restraints weight = 36420.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.118394 restraints weight = 33214.848| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30296 Z= 0.117 Angle : 0.575 11.389 41218 Z= 0.287 Chirality : 0.044 0.188 4594 Planarity : 0.004 0.047 5319 Dihedral : 4.040 36.264 4018 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.80 % Allowed : 20.17 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 3693 helix: 0.27 (0.18), residues: 879 sheet: -0.01 (0.19), residues: 631 loop : -1.21 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.027 0.001 TYR D1007 PHE 0.023 0.001 PHE B 559 TRP 0.017 0.001 TRP C 353 HIS 0.043 0.001 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00265 (30254) covalent geometry : angle 0.57230 (41134) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.34923 ( 84) hydrogen bonds : bond 0.03279 ( 875) hydrogen bonds : angle 5.01261 ( 2466) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 302 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.0566 (pp) REVERT: A 302 TRP cc_start: 0.2352 (OUTLIER) cc_final: -0.0345 (m100) REVERT: B 121 ASN cc_start: 0.2324 (OUTLIER) cc_final: -0.0093 (m110) REVERT: B 189 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7389 (mt) REVERT: B 301 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (t) REVERT: B 567 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7546 (ttm-80) REVERT: B 697 MET cc_start: 0.7845 (mtp) cc_final: 0.7403 (ttm) REVERT: B 725 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 818 ILE cc_start: 0.8421 (pt) cc_final: 0.7935 (mt) REVERT: B 868 GLU cc_start: 0.7959 (pm20) cc_final: 0.7570 (tm-30) REVERT: B 869 MET cc_start: 0.7019 (tpt) cc_final: 0.6710 (tpt) REVERT: B 988 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7893 (mp0) REVERT: B 1139 ASP cc_start: 0.7225 (t0) cc_final: 0.6642 (p0) REVERT: C 400 PHE cc_start: 0.3421 (OUTLIER) cc_final: 0.2039 (p90) REVERT: C 480 CYS cc_start: 0.1016 (OUTLIER) cc_final: -0.0183 (t) REVERT: C 951 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8544 (p) REVERT: C 954 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: C 1050 MET cc_start: 0.6767 (ptp) cc_final: 0.6492 (ptm) REVERT: D 90 VAL cc_start: 0.8836 (t) cc_final: 0.8595 (m) REVERT: D 153 MET cc_start: -0.2745 (ttp) cc_final: -0.3087 (mtm) REVERT: D 177 MET cc_start: -0.1871 (mmt) cc_final: -0.2829 (mmm) REVERT: D 436 TRP cc_start: 0.3820 (t60) cc_final: 0.3578 (t-100) REVERT: D 501 TYR cc_start: 0.5183 (OUTLIER) cc_final: 0.4267 (m-80) REVERT: D 699 LEU cc_start: 0.7288 (tt) cc_final: 0.6204 (mt) REVERT: D 725 GLU cc_start: 0.7469 (tt0) cc_final: 0.7162 (tt0) REVERT: D 864 LEU cc_start: 0.8474 (tt) cc_final: 0.7992 (tp) REVERT: D 965 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8117 (tp-100) REVERT: D 1017 GLU cc_start: 0.7480 (tp30) cc_final: 0.7134 (tp30) outliers start: 92 outliers final: 76 residues processed: 363 average time/residue: 0.1562 time to fit residues: 96.0323 Evaluate side-chains 377 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 291 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 123 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 207 optimal weight: 0.0770 chunk 315 optimal weight: 0.0070 chunk 20 optimal weight: 6.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C1002 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.144394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.116077 restraints weight = 112296.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.116624 restraints weight = 74550.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.117424 restraints weight = 54935.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118076 restraints weight = 39711.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.118063 restraints weight = 36315.310| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30296 Z= 0.114 Angle : 0.589 14.259 41218 Z= 0.293 Chirality : 0.044 0.187 4594 Planarity : 0.004 0.048 5319 Dihedral : 4.049 37.102 4018 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.65 % Allowed : 20.48 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 3693 helix: 0.29 (0.18), residues: 882 sheet: -0.02 (0.19), residues: 631 loop : -1.16 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 983 TYR 0.028 0.001 TYR D1007 PHE 0.022 0.001 PHE D 201 TRP 0.014 0.001 TRP C 353 HIS 0.009 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00260 (30254) covalent geometry : angle 0.58614 (41134) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.32739 ( 84) hydrogen bonds : bond 0.03287 ( 875) hydrogen bonds : angle 5.01232 ( 2466) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 307 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0252 (OUTLIER) cc_final: -0.0509 (pp) REVERT: A 302 TRP cc_start: 0.2004 (OUTLIER) cc_final: -0.0766 (m100) REVERT: A 323 MET cc_start: 0.4060 (tmm) cc_final: 0.3849 (tmm) REVERT: A 408 MET cc_start: 0.4250 (ppp) cc_final: 0.3982 (ppp) REVERT: B 121 ASN cc_start: 0.2401 (OUTLIER) cc_final: 0.0039 (m-40) REVERT: B 189 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7384 (mt) REVERT: B 301 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7656 (t) REVERT: B 567 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7533 (ttm-80) REVERT: B 697 MET cc_start: 0.7833 (mtp) cc_final: 0.7386 (ttm) REVERT: B 725 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7488 (tm-30) REVERT: B 818 ILE cc_start: 0.8373 (pt) cc_final: 0.7896 (mt) REVERT: B 988 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7906 (mp0) REVERT: B 1029 MET cc_start: 0.7960 (mmm) cc_final: 0.7611 (tpt) REVERT: B 1050 MET cc_start: 0.7637 (ptm) cc_final: 0.7402 (ptm) REVERT: B 1139 ASP cc_start: 0.7269 (t0) cc_final: 0.6641 (p0) REVERT: C 400 PHE cc_start: 0.3378 (OUTLIER) cc_final: 0.1924 (p90) REVERT: C 480 CYS cc_start: 0.0650 (OUTLIER) cc_final: -0.0434 (t) REVERT: C 951 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 954 HIS cc_start: 0.6657 (OUTLIER) cc_final: 0.6378 (m-70) REVERT: C 1050 MET cc_start: 0.6811 (ptp) cc_final: 0.6527 (ptm) REVERT: C 1120 THR cc_start: 0.7631 (p) cc_final: 0.7312 (t) REVERT: D 90 VAL cc_start: 0.8851 (t) cc_final: 0.8614 (m) REVERT: D 153 MET cc_start: -0.2768 (ttp) cc_final: -0.3096 (mtm) REVERT: D 177 MET cc_start: -0.1680 (mmt) cc_final: -0.2296 (mmm) REVERT: D 436 TRP cc_start: 0.3845 (t60) cc_final: 0.3576 (t-100) REVERT: D 501 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4230 (m-80) REVERT: D 699 LEU cc_start: 0.7372 (tt) cc_final: 0.6253 (mt) REVERT: D 725 GLU cc_start: 0.7434 (tt0) cc_final: 0.7112 (tt0) REVERT: D 864 LEU cc_start: 0.8570 (tt) cc_final: 0.8090 (tp) REVERT: D 965 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8126 (tp-100) REVERT: D 1017 GLU cc_start: 0.7476 (tp30) cc_final: 0.7146 (tp30) outliers start: 87 outliers final: 73 residues processed: 365 average time/residue: 0.1619 time to fit residues: 99.7847 Evaluate side-chains 374 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 291 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 182 optimal weight: 5.9990 chunk 274 optimal weight: 8.9990 chunk 339 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 266 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 353 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 49 HIS D 710 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN D1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.144169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.115901 restraints weight = 112891.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.116715 restraints weight = 78756.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.117013 restraints weight = 54869.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.117621 restraints weight = 45789.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.117770 restraints weight = 38963.386| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30296 Z= 0.111 Angle : 0.576 11.870 41218 Z= 0.288 Chirality : 0.044 0.185 4594 Planarity : 0.004 0.047 5319 Dihedral : 4.010 37.760 4018 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.56 % Allowed : 20.60 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 3693 helix: 0.36 (0.18), residues: 883 sheet: -0.10 (0.19), residues: 639 loop : -1.12 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1014 TYR 0.027 0.001 TYR D1007 PHE 0.023 0.001 PHE B 559 TRP 0.012 0.001 TRP C 886 HIS 0.008 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00252 (30254) covalent geometry : angle 0.57377 (41134) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.28277 ( 84) hydrogen bonds : bond 0.03203 ( 875) hydrogen bonds : angle 4.98080 ( 2466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.85 seconds wall clock time: 100 minutes 54.13 seconds (6054.13 seconds total)