Starting phenix.real_space_refine on Fri Mar 6 09:29:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w98_32361/03_2026/7w98_32361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w98_32361/03_2026/7w98_32361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w98_32361/03_2026/7w98_32361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w98_32361/03_2026/7w98_32361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w98_32361/03_2026/7w98_32361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w98_32361/03_2026/7w98_32361.map" } resolution = 3.6 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= 0.007 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18970 2.51 5 N 4982 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 211 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: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 6.12, per 1000 atoms: 0.21 Number of scatterers: 29737 At special positions: 0 Unit cell: (157.392, 171.601, 241.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5642 8.00 N 4982 7.00 C 18970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 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=2.03 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 A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 2.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7076 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 50 sheets defined 30.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.956A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.721A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.598A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.723A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.529A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.910A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.591A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.784A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.537A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.572A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.706A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.857A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.501A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 removed outlier: 3.644A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.704A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.828A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.194A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.639A pdb=" N ALA D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.533A pdb=" N SER D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.607A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.500A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.578A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.653A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.713A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.592A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.758A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.709A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.793A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.742A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.569A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.885A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.520A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.161A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.722A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.893A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.733A pdb=" N THR D 593 " --> pdb=" O GLU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.221A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.999A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.691A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.718A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.649A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.520A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.536A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.117A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.776A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.618A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.507A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 3.784A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.694A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.459A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.307A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.761A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.548A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.623A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.711A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B 537 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 552 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.777A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.464A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.912A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.186A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.529A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.521A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.927A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.612A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.612A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.610A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.219A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.844A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.654A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.654A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.939A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.925A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.282A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.899A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.587A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.767A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.836A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.393A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.861A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.635A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 721 removed outlier: 6.792A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 724 through 728 removed outlier: 3.664A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.885A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3174 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: 7.38 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9633 1.35 - 1.47: 7572 1.47 - 1.59: 13045 1.59 - 1.71: 0 1.71 - 1.83: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" N GLN A 14 " pdb=" CA GLN A 14 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" C SER A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.18e+00 bond pdb=" N SER D 19 " pdb=" CA SER D 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN B 14 " pdb=" CA GLN B 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 40013 1.28 - 2.55: 1135 2.55 - 3.83: 103 3.83 - 5.10: 131 5.10 - 6.38: 14 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 111.56 108.66 2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" CA ILE C 664 " pdb=" C ILE C 664 " pdb=" N PRO C 665 " ideal model delta sigma weight residual 118.12 120.36 -2.24 8.10e-01 1.52e+00 7.64e+00 angle pdb=" CA ILE C 664 " pdb=" C ILE C 664 " pdb=" O ILE C 664 " ideal model delta sigma weight residual 120.88 119.02 1.86 6.80e-01 2.16e+00 7.46e+00 angle pdb=" N VAL D 581 " pdb=" CA VAL D 581 " pdb=" CB VAL D 581 " ideal model delta sigma weight residual 112.21 109.22 2.99 1.10e+00 8.26e-01 7.41e+00 angle pdb=" C GLU D 145 " pdb=" N PRO D 146 " pdb=" CA PRO D 146 " ideal model delta sigma weight residual 127.00 133.12 -6.12 2.40e+00 1.74e-01 6.49e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16910 18.00 - 35.99: 996 35.99 - 53.99: 148 53.99 - 71.99: 53 71.99 - 89.98: 29 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 47.46 45.54 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 52.92 40.08 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.94 38.94 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3031 0.032 - 0.064: 1090 0.064 - 0.096: 227 0.096 - 0.128: 242 0.128 - 0.160: 26 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE A 896 " pdb=" N ILE A 896 " pdb=" C ILE A 896 " pdb=" CB ILE A 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE B 896 " pdb=" N ILE B 896 " pdb=" C ILE B 896 " pdb=" CB ILE B 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO C 230 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 130 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C VAL C 130 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL C 130 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS C 131 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 714 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 715 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 715 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 715 " 0.019 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 270 2.61 - 3.18: 25330 3.18 - 3.76: 44166 3.76 - 4.33: 63213 4.33 - 4.90: 104667 Nonbonded interactions: 237646 Sorted by model distance: nonbonded pdb=" OG1 THR A 883 " pdb=" OH TYR C 707 " model vdw 2.038 3.040 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 2.078 3.040 nonbonded pdb=" O GLN A 755 " pdb=" OG SER C 968 " model vdw 2.100 3.040 nonbonded pdb=" O GLN B 755 " pdb=" OG SER A 968 " model vdw 2.105 3.040 nonbonded pdb=" OG SER B 711 " pdb=" OE1 GLN C 895 " model vdw 2.128 3.040 ... (remaining 237641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.860 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 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 : 0.003 0.042 30486 Z= 0.163 Angle : 0.575 6.376 41480 Z= 0.321 Chirality : 0.041 0.160 4616 Planarity : 0.003 0.042 5375 Dihedral : 12.487 89.982 10934 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.03 % Allowed : 1.42 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.11), residues: 3733 helix: -2.22 (0.12), residues: 1002 sheet: -2.21 (0.17), residues: 665 loop : -2.17 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.008 0.001 TYR B 873 PHE 0.011 0.001 PHE A 562 TRP 0.005 0.001 TRP D 203 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00345 (30444) covalent geometry : angle 0.57393 (41396) SS BOND : bond 0.00279 ( 42) SS BOND : angle 0.81665 ( 84) hydrogen bonds : bond 0.27394 ( 1130) hydrogen bonds : angle 9.29155 ( 3174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 761 time to evaluate : 1.098 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: B 117 LEU cc_start: 0.7976 (mp) cc_final: 0.7630 (tp) REVERT: B 129 LYS cc_start: 0.8317 (mttt) cc_final: 0.8102 (mtpp) REVERT: B 143 VAL cc_start: 0.6342 (t) cc_final: 0.5746 (t) REVERT: B 458 LYS cc_start: 0.5962 (mppt) cc_final: 0.5164 (pttm) REVERT: B 708 SER cc_start: 0.7260 (t) cc_final: 0.6812 (m) REVERT: B 752 LEU cc_start: 0.9290 (mp) cc_final: 0.8922 (tp) REVERT: B 756 TYR cc_start: 0.8576 (m-80) cc_final: 0.8090 (m-80) REVERT: B 859 THR cc_start: 0.7397 (m) cc_final: 0.7196 (t) REVERT: B 918 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 1073 LYS cc_start: 0.8492 (mttt) cc_final: 0.8103 (mtpt) REVERT: A 58 PHE cc_start: 0.8306 (m-10) cc_final: 0.8052 (m-80) REVERT: A 119 ILE cc_start: 0.8698 (mt) cc_final: 0.8450 (mt) REVERT: A 216 LEU cc_start: 0.6490 (mt) cc_final: 0.6263 (mt) REVERT: A 298 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 340 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7119 (pt0) REVERT: A 356 LYS cc_start: 0.5100 (ttmm) cc_final: 0.4501 (mmmm) REVERT: A 389 ASP cc_start: 0.6236 (m-30) cc_final: 0.5732 (m-30) REVERT: A 703 ASN cc_start: 0.7636 (m-40) cc_final: 0.7387 (t0) REVERT: A 751 ASN cc_start: 0.8820 (m-40) cc_final: 0.7948 (m110) REVERT: A 752 LEU cc_start: 0.8921 (mt) cc_final: 0.8344 (mt) REVERT: A 973 ILE cc_start: 0.9343 (tt) cc_final: 0.9140 (tp) REVERT: A 979 ASP cc_start: 0.8558 (m-30) cc_final: 0.8276 (m-30) REVERT: A 984 LEU cc_start: 0.7725 (mp) cc_final: 0.6815 (mt) REVERT: D 32 PHE cc_start: 0.7028 (t80) cc_final: 0.6801 (t80) REVERT: D 323 MET cc_start: 0.4041 (mmt) cc_final: 0.3052 (mmt) REVERT: D 383 MET cc_start: 0.6513 (mtp) cc_final: 0.6308 (ppp) REVERT: D 557 MET cc_start: 0.3220 (ttp) cc_final: 0.2939 (ptm) REVERT: C 19 ARG cc_start: 0.6689 (ptp-170) cc_final: 0.6351 (tpm170) REVERT: C 55 PHE cc_start: 0.8153 (m-80) cc_final: 0.7412 (m-80) REVERT: C 86 PHE cc_start: 0.5869 (t80) cc_final: 0.5617 (t80) REVERT: C 104 TRP cc_start: 0.7976 (m-90) cc_final: 0.7297 (m100) REVERT: C 229 LEU cc_start: 0.8658 (mt) cc_final: 0.8447 (mt) REVERT: C 237 ARG cc_start: 0.6232 (mtm180) cc_final: 0.5735 (mpp80) REVERT: C 270 LEU cc_start: 0.8407 (mp) cc_final: 0.8147 (mp) REVERT: C 979 ASP cc_start: 0.8565 (m-30) cc_final: 0.8188 (m-30) REVERT: C 981 LEU cc_start: 0.8165 (tp) cc_final: 0.7899 (tp) REVERT: C 983 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7611 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 762 average time/residue: 0.1807 time to fit residues: 218.2777 Evaluate side-chains 375 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 207 HIS B 218 GLN B 317 ASN B 460 ASN B 481 ASN B 703 ASN B 907 ASN B 949 GLN B 955 ASN B1135 ASN A 30 ASN A 66 HIS A 99 ASN A 149 ASN A 188 ASN A 493 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 949 GLN A1088 HIS D 134 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 137 ASN C 450 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 764 ASN C 787 GLN C 935 GLN C1002 GLN C1083 HIS C1113 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.139163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.110875 restraints weight = 100843.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.113124 restraints weight = 50209.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.114443 restraints weight = 29568.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.115140 restraints weight = 21161.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.115801 restraints weight = 17214.469| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30486 Z= 0.256 Angle : 0.725 10.644 41480 Z= 0.380 Chirality : 0.049 0.227 4616 Planarity : 0.005 0.047 5375 Dihedral : 4.788 23.332 4050 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.85 % Allowed : 10.30 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3733 helix: -0.11 (0.15), residues: 1005 sheet: -1.37 (0.18), residues: 674 loop : -1.62 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 567 TYR 0.021 0.002 TYR C 91 PHE 0.024 0.002 PHE A 592 TRP 0.023 0.002 TRP D 349 HIS 0.007 0.002 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00582 (30444) covalent geometry : angle 0.72241 (41396) SS BOND : bond 0.00407 ( 42) SS BOND : angle 1.59334 ( 84) hydrogen bonds : bond 0.05067 ( 1130) hydrogen bonds : angle 6.02557 ( 3174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 441 time to evaluate : 1.017 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: B 128 ILE cc_start: 0.8600 (mp) cc_final: 0.8340 (mp) REVERT: B 195 LYS cc_start: 0.7554 (pptt) cc_final: 0.6677 (pttt) REVERT: B 286 THR cc_start: 0.8786 (p) cc_final: 0.8468 (t) REVERT: B 408 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3383 (tmm-80) REVERT: B 752 LEU cc_start: 0.9362 (mp) cc_final: 0.9020 (tp) REVERT: B 756 TYR cc_start: 0.8956 (m-80) cc_final: 0.8607 (m-80) REVERT: B 870 ILE cc_start: 0.9264 (mm) cc_final: 0.8934 (mt) REVERT: B 900 MET cc_start: 0.8561 (mmt) cc_final: 0.7659 (mpp) REVERT: B 983 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7364 (mtp180) REVERT: B 1073 LYS cc_start: 0.8198 (mttt) cc_final: 0.7988 (mtpt) REVERT: B 1114 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 177 MET cc_start: 0.2189 (mtp) cc_final: -0.0252 (mmt) REVERT: A 265 TYR cc_start: 0.7102 (p90) cc_final: 0.6348 (p90) REVERT: A 389 ASP cc_start: 0.6693 (m-30) cc_final: 0.5773 (m-30) REVERT: A 552 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 751 ASN cc_start: 0.8893 (m-40) cc_final: 0.8606 (m-40) REVERT: A 755 GLN cc_start: 0.7998 (mp10) cc_final: 0.7741 (mp10) REVERT: A 979 ASP cc_start: 0.8799 (m-30) cc_final: 0.8364 (m-30) REVERT: A 1031 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 1110 TYR cc_start: 0.8759 (t80) cc_final: 0.8473 (t80) REVERT: D 190 MET cc_start: -0.1179 (tpp) cc_final: -0.1398 (tpp) REVERT: D 202 TYR cc_start: 0.6296 (t80) cc_final: 0.5862 (m-80) REVERT: D 582 ARG cc_start: 0.6665 (mpt180) cc_final: 0.5310 (mmp-170) REVERT: C 19 ARG cc_start: 0.6315 (ptp-170) cc_final: 0.5874 (tpt170) REVERT: C 55 PHE cc_start: 0.7789 (m-80) cc_final: 0.7259 (m-80) REVERT: C 390 LEU cc_start: 0.6674 (mp) cc_final: 0.5930 (mt) REVERT: C 412 PRO cc_start: 0.4303 (Cg_endo) cc_final: 0.4008 (Cg_exo) REVERT: C 979 ASP cc_start: 0.8380 (m-30) cc_final: 0.8095 (m-30) REVERT: C 983 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7758 (ttm-80) REVERT: C 994 ASP cc_start: 0.8261 (t70) cc_final: 0.7874 (t0) outliers start: 94 outliers final: 50 residues processed: 510 average time/residue: 0.1734 time to fit residues: 142.2949 Evaluate side-chains 372 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1055 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 203 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 253 optimal weight: 10.0000 chunk 288 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN B 764 ASN A 99 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 764 ASN C 914 ASN C 957 GLN C1083 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.141928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.114023 restraints weight = 99874.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.116129 restraints weight = 50456.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.117161 restraints weight = 32058.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.118956 restraints weight = 23510.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.119069 restraints weight = 17715.075| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30486 Z= 0.116 Angle : 0.537 8.730 41480 Z= 0.280 Chirality : 0.044 0.262 4616 Planarity : 0.004 0.049 5375 Dihedral : 4.108 20.710 4050 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.30 % Allowed : 12.99 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.92 (0.13), residues: 3733 helix: 0.89 (0.17), residues: 1010 sheet: -0.85 (0.19), residues: 669 loop : -1.30 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.021 0.001 TYR D 217 PHE 0.025 0.001 PHE A 79 TRP 0.035 0.002 TRP B 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00254 (30444) covalent geometry : angle 0.53540 (41396) SS BOND : bond 0.00346 ( 42) SS BOND : angle 1.03298 ( 84) hydrogen bonds : bond 0.04029 ( 1130) hydrogen bonds : angle 5.34569 ( 3174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 401 time to evaluate : 0.997 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: B 195 LYS cc_start: 0.7589 (pptt) cc_final: 0.6743 (pttt) REVERT: B 223 LEU cc_start: 0.7974 (mp) cc_final: 0.7120 (mt) REVERT: B 286 THR cc_start: 0.8783 (p) cc_final: 0.8434 (t) REVERT: B 458 LYS cc_start: 0.5898 (mptt) cc_final: 0.5644 (pttm) REVERT: B 664 ILE cc_start: 0.8871 (mt) cc_final: 0.8581 (mm) REVERT: B 752 LEU cc_start: 0.9379 (mp) cc_final: 0.9050 (tp) REVERT: B 756 TYR cc_start: 0.8974 (m-80) cc_final: 0.8689 (m-80) REVERT: B 870 ILE cc_start: 0.9235 (mm) cc_final: 0.8924 (mt) REVERT: B 900 MET cc_start: 0.8483 (mmt) cc_final: 0.7567 (mpp) REVERT: B 957 GLN cc_start: 0.7536 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 983 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7444 (mtp180) REVERT: B 995 ARG cc_start: 0.8624 (mtp85) cc_final: 0.7987 (mtm-85) REVERT: A 177 MET cc_start: 0.1450 (mtp) cc_final: -0.0382 (mmt) REVERT: A 552 LEU cc_start: 0.8592 (mm) cc_final: 0.8350 (mm) REVERT: A 787 GLN cc_start: 0.8013 (pm20) cc_final: 0.7659 (pm20) REVERT: A 979 ASP cc_start: 0.8851 (m-30) cc_final: 0.8458 (m-30) REVERT: A 1110 TYR cc_start: 0.8756 (t80) cc_final: 0.8435 (t80) REVERT: D 57 GLU cc_start: 0.2295 (OUTLIER) cc_final: 0.2064 (pt0) REVERT: D 239 HIS cc_start: 0.3753 (m-70) cc_final: 0.3533 (m170) REVERT: D 613 TYR cc_start: 0.2007 (p90) cc_final: 0.1435 (p90) REVERT: C 19 ARG cc_start: 0.6122 (ptp-170) cc_final: 0.5878 (tpt170) REVERT: C 390 LEU cc_start: 0.6857 (mp) cc_final: 0.5901 (tp) REVERT: C 664 ILE cc_start: 0.8902 (mm) cc_final: 0.8614 (mm) REVERT: C 874 THR cc_start: 0.9185 (m) cc_final: 0.8969 (p) REVERT: C 962 LEU cc_start: 0.8605 (tp) cc_final: 0.8390 (tt) REVERT: C 979 ASP cc_start: 0.8284 (m-30) cc_final: 0.7983 (m-30) REVERT: C 983 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8058 (ttm-80) REVERT: C 990 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: C 994 ASP cc_start: 0.8057 (t70) cc_final: 0.7775 (t0) REVERT: C 1019 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8375 (ttp80) REVERT: C 1072 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7843 (mt-10) outliers start: 76 outliers final: 40 residues processed: 454 average time/residue: 0.1652 time to fit residues: 122.7622 Evaluate side-chains 365 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 322 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 130 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 243 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 362 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 703 ASN A 703 ASN A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.138474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.110374 restraints weight = 99658.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112494 restraints weight = 49681.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113959 restraints weight = 30021.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.114691 restraints weight = 21368.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.115084 restraints weight = 17308.604| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30486 Z= 0.168 Angle : 0.585 10.945 41480 Z= 0.303 Chirality : 0.044 0.175 4616 Planarity : 0.004 0.047 5375 Dihedral : 4.352 21.971 4050 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.09 % Allowed : 13.75 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 3733 helix: 1.17 (0.17), residues: 1003 sheet: -0.58 (0.19), residues: 663 loop : -1.20 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 319 TYR 0.023 0.002 TYR B 144 PHE 0.023 0.002 PHE A 79 TRP 0.025 0.002 TRP C 104 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00384 (30444) covalent geometry : angle 0.58348 (41396) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.17796 ( 84) hydrogen bonds : bond 0.04066 ( 1130) hydrogen bonds : angle 5.25469 ( 3174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 354 time to evaluate : 1.157 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: B 128 ILE cc_start: 0.8611 (mp) cc_final: 0.8371 (pt) REVERT: B 223 LEU cc_start: 0.7738 (mp) cc_final: 0.7172 (mt) REVERT: B 297 SER cc_start: 0.8967 (m) cc_final: 0.8621 (p) REVERT: B 408 ARG cc_start: 0.4448 (OUTLIER) cc_final: 0.3956 (tmm-80) REVERT: B 458 LYS cc_start: 0.6396 (mptt) cc_final: 0.5663 (pttm) REVERT: B 664 ILE cc_start: 0.8803 (mt) cc_final: 0.8601 (mm) REVERT: B 752 LEU cc_start: 0.9416 (mp) cc_final: 0.9108 (tp) REVERT: B 900 MET cc_start: 0.8676 (mmt) cc_final: 0.7837 (mpp) REVERT: B 957 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 983 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7641 (mtp180) REVERT: B 1030 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8613 (t) REVERT: A 177 MET cc_start: 0.0844 (mtp) cc_final: -0.0614 (mmt) REVERT: A 265 TYR cc_start: 0.6966 (p90) cc_final: 0.6544 (p90) REVERT: A 552 LEU cc_start: 0.8621 (mm) cc_final: 0.8323 (mm) REVERT: A 787 GLN cc_start: 0.8069 (pm20) cc_final: 0.7609 (pm20) REVERT: A 900 MET cc_start: 0.8684 (mtm) cc_final: 0.8028 (mtm) REVERT: A 925 ASN cc_start: 0.8412 (m-40) cc_final: 0.8009 (m-40) REVERT: A 957 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 1041 ASP cc_start: 0.7413 (t0) cc_final: 0.7011 (t0) REVERT: A 1110 TYR cc_start: 0.8825 (t80) cc_final: 0.8452 (t80) REVERT: C 19 ARG cc_start: 0.6070 (ptp-170) cc_final: 0.5449 (mmt180) REVERT: C 177 MET cc_start: 0.2734 (tpp) cc_final: 0.2199 (tpp) REVERT: C 664 ILE cc_start: 0.8971 (mm) cc_final: 0.8617 (mm) REVERT: C 776 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8560 (ttpp) REVERT: C 979 ASP cc_start: 0.8298 (m-30) cc_final: 0.8037 (m-30) REVERT: C 983 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: C 994 ASP cc_start: 0.8269 (t70) cc_final: 0.7816 (t0) REVERT: C 1072 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7908 (mt-10) outliers start: 102 outliers final: 65 residues processed: 430 average time/residue: 0.1713 time to fit residues: 120.4191 Evaluate side-chains 378 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 310 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 118 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 703 ASN B 919 ASN A 703 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.137398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109424 restraints weight = 99844.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.111232 restraints weight = 48627.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.112733 restraints weight = 31359.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.113365 restraints weight = 21891.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.114203 restraints weight = 17679.816| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30486 Z= 0.163 Angle : 0.571 9.035 41480 Z= 0.294 Chirality : 0.044 0.161 4616 Planarity : 0.004 0.043 5375 Dihedral : 4.390 26.546 4050 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.12 % Allowed : 15.08 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.13), residues: 3733 helix: 1.32 (0.17), residues: 998 sheet: -0.52 (0.19), residues: 663 loop : -1.16 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1019 TYR 0.023 0.002 TYR A 449 PHE 0.021 0.002 PHE C 392 TRP 0.030 0.002 TRP C 104 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00370 (30444) covalent geometry : angle 0.56878 (41396) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.28072 ( 84) hydrogen bonds : bond 0.03921 ( 1130) hydrogen bonds : angle 5.16265 ( 3174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 343 time to evaluate : 1.120 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: B 223 LEU cc_start: 0.7919 (mp) cc_final: 0.7305 (mt) REVERT: B 297 SER cc_start: 0.8963 (m) cc_final: 0.8617 (p) REVERT: B 752 LEU cc_start: 0.9428 (mp) cc_final: 0.9141 (tp) REVERT: B 900 MET cc_start: 0.8670 (mmt) cc_final: 0.7840 (mpp) REVERT: B 957 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 983 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7672 (mtp180) REVERT: B 1030 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8684 (t) REVERT: A 269 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.5107 (m-80) REVERT: A 552 LEU cc_start: 0.8620 (mm) cc_final: 0.8310 (mm) REVERT: A 756 TYR cc_start: 0.8878 (m-80) cc_final: 0.8606 (m-10) REVERT: A 787 GLN cc_start: 0.8174 (pm20) cc_final: 0.7769 (pm20) REVERT: A 900 MET cc_start: 0.8733 (mtm) cc_final: 0.8047 (mtm) REVERT: A 925 ASN cc_start: 0.8366 (m-40) cc_final: 0.7919 (m-40) REVERT: A 957 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 1041 ASP cc_start: 0.7484 (t0) cc_final: 0.6978 (t0) REVERT: A 1110 TYR cc_start: 0.8860 (t80) cc_final: 0.8445 (t80) REVERT: D 587 TYR cc_start: 0.0015 (t80) cc_final: -0.0692 (t80) REVERT: C 19 ARG cc_start: 0.5911 (ptp-170) cc_final: 0.5401 (tpt170) REVERT: C 177 MET cc_start: 0.3046 (tpp) cc_final: 0.2529 (ttp) REVERT: C 664 ILE cc_start: 0.8954 (mm) cc_final: 0.8702 (mm) REVERT: C 776 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8546 (ttpp) REVERT: C 979 ASP cc_start: 0.8144 (m-30) cc_final: 0.7901 (m-30) REVERT: C 983 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8070 (ttm-80) REVERT: C 994 ASP cc_start: 0.8276 (t70) cc_final: 0.7791 (t0) REVERT: C 1072 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7836 (mt-10) outliers start: 103 outliers final: 69 residues processed: 414 average time/residue: 0.1611 time to fit residues: 110.1129 Evaluate side-chains 377 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 175 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 67 optimal weight: 0.0570 chunk 163 optimal weight: 0.0370 chunk 31 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 345 optimal weight: 0.4980 chunk 105 optimal weight: 0.0870 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN A 703 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 950 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.141350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113998 restraints weight = 98972.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.116046 restraints weight = 48079.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.117677 restraints weight = 30741.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.118221 restraints weight = 21023.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.118708 restraints weight = 17097.325| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30486 Z= 0.095 Angle : 0.515 13.082 41480 Z= 0.263 Chirality : 0.042 0.183 4616 Planarity : 0.003 0.042 5375 Dihedral : 3.969 26.599 4050 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.91 % Allowed : 16.81 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3733 helix: 1.59 (0.17), residues: 999 sheet: -0.28 (0.19), residues: 668 loop : -1.00 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.020 0.001 TYR A 265 PHE 0.019 0.001 PHE D 315 TRP 0.020 0.001 TRP C 104 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00205 (30444) covalent geometry : angle 0.51312 (41396) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.10002 ( 84) hydrogen bonds : bond 0.03264 ( 1130) hydrogen bonds : angle 4.77519 ( 3174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 369 time to evaluate : 1.016 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: B 176 LEU cc_start: 0.2447 (OUTLIER) cc_final: 0.2202 (pp) REVERT: B 195 LYS cc_start: 0.7658 (pptt) cc_final: 0.7156 (pttt) REVERT: B 223 LEU cc_start: 0.7823 (mp) cc_final: 0.7306 (mt) REVERT: B 297 SER cc_start: 0.8915 (m) cc_final: 0.8561 (p) REVERT: B 708 SER cc_start: 0.7529 (t) cc_final: 0.7259 (m) REVERT: B 752 LEU cc_start: 0.9427 (mp) cc_final: 0.9174 (tp) REVERT: B 900 MET cc_start: 0.8568 (mmt) cc_final: 0.7831 (mpp) REVERT: B 957 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 983 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7707 (ttt-90) REVERT: B 1030 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8702 (t) REVERT: A 177 MET cc_start: 0.0102 (mtt) cc_final: -0.1194 (mtt) REVERT: A 265 TYR cc_start: 0.6931 (p90) cc_final: 0.6573 (p90) REVERT: A 269 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5225 (m-80) REVERT: A 552 LEU cc_start: 0.8617 (mm) cc_final: 0.8370 (mm) REVERT: A 664 ILE cc_start: 0.8868 (mm) cc_final: 0.8662 (mm) REVERT: A 787 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: A 900 MET cc_start: 0.8411 (mtm) cc_final: 0.7771 (mtm) REVERT: A 925 ASN cc_start: 0.8304 (m-40) cc_final: 0.7873 (m-40) REVERT: A 957 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7507 (tm-30) REVERT: A 1041 ASP cc_start: 0.7460 (t0) cc_final: 0.7148 (t0) REVERT: A 1110 TYR cc_start: 0.8804 (t80) cc_final: 0.8447 (t80) REVERT: D 270 MET cc_start: 0.1390 (mpp) cc_final: 0.0987 (mpp) REVERT: D 366 MET cc_start: 0.4286 (mtp) cc_final: 0.3952 (mtm) REVERT: C 19 ARG cc_start: 0.5810 (ptp-170) cc_final: 0.5430 (mmp80) REVERT: C 177 MET cc_start: 0.2821 (tpp) cc_final: 0.2460 (ttp) REVERT: C 664 ILE cc_start: 0.8831 (mm) cc_final: 0.8594 (mm) REVERT: C 979 ASP cc_start: 0.8179 (m-30) cc_final: 0.7875 (m-30) REVERT: C 983 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8067 (ttm-80) REVERT: C 994 ASP cc_start: 0.8046 (t70) cc_final: 0.7811 (t0) REVERT: C 1019 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8350 (ttp80) REVERT: C 1072 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (mt-10) outliers start: 63 outliers final: 40 residues processed: 406 average time/residue: 0.1634 time to fit residues: 109.9012 Evaluate side-chains 365 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 135 optimal weight: 0.0980 chunk 346 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 171 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 919 ASN A 703 ASN A 762 GLN A 787 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.137866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110095 restraints weight = 100070.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112326 restraints weight = 49584.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.113651 restraints weight = 29621.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.114288 restraints weight = 21008.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.114982 restraints weight = 17311.796| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30486 Z= 0.147 Angle : 0.567 11.240 41480 Z= 0.290 Chirality : 0.043 0.247 4616 Planarity : 0.004 0.039 5375 Dihedral : 4.183 26.201 4050 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.57 % Allowed : 17.23 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3733 helix: 1.51 (0.17), residues: 1009 sheet: -0.24 (0.19), residues: 659 loop : -1.00 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1019 TYR 0.035 0.002 TYR C 904 PHE 0.023 0.002 PHE B 927 TRP 0.033 0.002 TRP C 886 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00336 (30444) covalent geometry : angle 0.56487 (41396) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.18828 ( 84) hydrogen bonds : bond 0.03718 ( 1130) hydrogen bonds : angle 4.87763 ( 3174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 321 time to evaluate : 1.033 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: B 119 ILE cc_start: 0.8489 (mm) cc_final: 0.8232 (tp) REVERT: B 223 LEU cc_start: 0.7880 (mp) cc_final: 0.7248 (mt) REVERT: B 297 SER cc_start: 0.8954 (m) cc_final: 0.8580 (p) REVERT: B 408 ARG cc_start: 0.4492 (OUTLIER) cc_final: 0.4245 (tmm-80) REVERT: B 592 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: B 752 LEU cc_start: 0.9444 (mp) cc_final: 0.9158 (tp) REVERT: B 957 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 983 ARG cc_start: 0.7995 (ttt180) cc_final: 0.7693 (ttt-90) REVERT: B 1030 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8731 (t) REVERT: A 177 MET cc_start: -0.0038 (mtt) cc_final: -0.0633 (mtt) REVERT: A 265 TYR cc_start: 0.6998 (p90) cc_final: 0.6670 (p90) REVERT: A 269 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.5142 (m-80) REVERT: A 552 LEU cc_start: 0.8597 (mm) cc_final: 0.8304 (mm) REVERT: A 780 GLU cc_start: 0.8242 (tt0) cc_final: 0.8026 (tt0) REVERT: A 900 MET cc_start: 0.8654 (mtm) cc_final: 0.7896 (mtm) REVERT: A 925 ASN cc_start: 0.8400 (m-40) cc_final: 0.7969 (m-40) REVERT: A 957 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 1017 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7835 (mm-30) REVERT: A 1041 ASP cc_start: 0.7558 (t0) cc_final: 0.7183 (t0) REVERT: A 1050 MET cc_start: 0.8131 (ptm) cc_final: 0.7891 (ptm) REVERT: A 1110 TYR cc_start: 0.8871 (t80) cc_final: 0.8461 (t80) REVERT: D 249 MET cc_start: 0.1534 (mtp) cc_final: 0.0243 (ptt) REVERT: D 581 VAL cc_start: 0.1488 (OUTLIER) cc_final: 0.1182 (m) REVERT: C 19 ARG cc_start: 0.5819 (ptp-170) cc_final: 0.5262 (mmp80) REVERT: C 177 MET cc_start: 0.3004 (tpp) cc_final: 0.2446 (ttp) REVERT: C 664 ILE cc_start: 0.8961 (mm) cc_final: 0.8688 (mm) REVERT: C 776 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8605 (ttpp) REVERT: C 979 ASP cc_start: 0.8165 (m-30) cc_final: 0.7960 (m-30) REVERT: C 983 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: C 994 ASP cc_start: 0.8232 (t70) cc_final: 0.7946 (t0) REVERT: C 1002 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: C 1072 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7843 (mt-10) outliers start: 85 outliers final: 58 residues processed: 373 average time/residue: 0.1661 time to fit residues: 101.5812 Evaluate side-chains 367 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 66 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 chunk 37 optimal weight: 0.0670 chunk 246 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 210 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN A 787 GLN A 950 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.139527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112060 restraints weight = 99666.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.114037 restraints weight = 48465.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.115770 restraints weight = 31539.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.116303 restraints weight = 21398.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.116662 restraints weight = 17191.321| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30486 Z= 0.105 Angle : 0.534 12.007 41480 Z= 0.272 Chirality : 0.042 0.224 4616 Planarity : 0.003 0.040 5375 Dihedral : 4.027 25.592 4050 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.24 % Allowed : 17.53 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3733 helix: 1.62 (0.17), residues: 1002 sheet: -0.11 (0.20), residues: 661 loop : -0.89 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1019 TYR 0.017 0.001 TYR A 449 PHE 0.022 0.001 PHE B 927 TRP 0.028 0.001 TRP C 104 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00235 (30444) covalent geometry : angle 0.53220 (41396) SS BOND : bond 0.00256 ( 42) SS BOND : angle 1.09333 ( 84) hydrogen bonds : bond 0.03348 ( 1130) hydrogen bonds : angle 4.69131 ( 3174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 1.100 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: B 176 LEU cc_start: 0.2471 (OUTLIER) cc_final: 0.2129 (pp) REVERT: B 191 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: B 195 LYS cc_start: 0.7638 (pptt) cc_final: 0.7199 (pttt) REVERT: B 223 LEU cc_start: 0.7908 (mp) cc_final: 0.7295 (mt) REVERT: B 297 SER cc_start: 0.8931 (m) cc_final: 0.8589 (p) REVERT: B 408 ARG cc_start: 0.4861 (OUTLIER) cc_final: 0.4482 (tmm-80) REVERT: B 592 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: B 752 LEU cc_start: 0.9447 (mp) cc_final: 0.9210 (tp) REVERT: B 957 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 983 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7761 (ttt-90) REVERT: B 1030 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8748 (t) REVERT: A 177 MET cc_start: -0.1320 (mtt) cc_final: -0.2461 (mtt) REVERT: A 265 TYR cc_start: 0.6947 (p90) cc_final: 0.6617 (p90) REVERT: A 269 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.5244 (m-80) REVERT: A 552 LEU cc_start: 0.8591 (mm) cc_final: 0.8330 (mm) REVERT: A 664 ILE cc_start: 0.8890 (mm) cc_final: 0.8668 (mm) REVERT: A 780 GLU cc_start: 0.8203 (tt0) cc_final: 0.7989 (tt0) REVERT: A 900 MET cc_start: 0.8540 (mtm) cc_final: 0.7812 (mtm) REVERT: A 925 ASN cc_start: 0.8331 (m-40) cc_final: 0.7886 (m-40) REVERT: A 957 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 1041 ASP cc_start: 0.7563 (t0) cc_final: 0.7195 (t0) REVERT: A 1110 TYR cc_start: 0.8832 (t80) cc_final: 0.8411 (t80) REVERT: D 249 MET cc_start: 0.1436 (mtp) cc_final: 0.0158 (ptt) REVERT: D 581 VAL cc_start: 0.1557 (OUTLIER) cc_final: 0.1256 (m) REVERT: C 19 ARG cc_start: 0.5447 (ptp-170) cc_final: 0.5209 (mmp80) REVERT: C 177 MET cc_start: 0.3088 (tpp) cc_final: 0.2592 (ttp) REVERT: C 274 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8399 (p) REVERT: C 664 ILE cc_start: 0.8918 (mm) cc_final: 0.8657 (mm) REVERT: C 764 ASN cc_start: 0.8187 (m-40) cc_final: 0.7887 (m110) REVERT: C 776 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8599 (ttpp) REVERT: C 983 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7140 (ttm-80) REVERT: C 994 ASP cc_start: 0.8115 (t70) cc_final: 0.7878 (t0) REVERT: C 1002 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: C 1072 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7663 (mt-10) outliers start: 74 outliers final: 46 residues processed: 377 average time/residue: 0.1661 time to fit residues: 103.0473 Evaluate side-chains 363 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 200 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 363 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.137317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.109534 restraints weight = 100118.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.111720 restraints weight = 49722.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.113042 restraints weight = 30126.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.113669 restraints weight = 21449.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.114380 restraints weight = 17691.490| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30486 Z= 0.148 Angle : 0.570 11.259 41480 Z= 0.292 Chirality : 0.043 0.215 4616 Planarity : 0.004 0.039 5375 Dihedral : 4.228 25.437 4050 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 17.69 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.14), residues: 3733 helix: 1.44 (0.17), residues: 1015 sheet: -0.15 (0.20), residues: 660 loop : -0.92 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1019 TYR 0.021 0.001 TYR A 904 PHE 0.024 0.002 PHE C 168 TRP 0.030 0.002 TRP C 886 HIS 0.009 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00339 (30444) covalent geometry : angle 0.56786 (41396) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.22120 ( 84) hydrogen bonds : bond 0.03670 ( 1130) hydrogen bonds : angle 4.80518 ( 3174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 319 time to evaluate : 0.910 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: B 176 LEU cc_start: 0.2232 (OUTLIER) cc_final: 0.1854 (pp) REVERT: B 191 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: B 223 LEU cc_start: 0.7822 (mp) cc_final: 0.7106 (mt) REVERT: B 297 SER cc_start: 0.8968 (m) cc_final: 0.8513 (t) REVERT: B 408 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.4255 (tmm-80) REVERT: B 417 LYS cc_start: 0.3540 (tptt) cc_final: 0.2943 (ptmt) REVERT: B 592 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7057 (m-10) REVERT: B 957 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 983 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7701 (ttt-90) REVERT: B 1030 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8709 (t) REVERT: A 265 TYR cc_start: 0.6850 (p90) cc_final: 0.6587 (p90) REVERT: A 269 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: A 703 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8354 (t0) REVERT: A 780 GLU cc_start: 0.8283 (tt0) cc_final: 0.8071 (tt0) REVERT: A 900 MET cc_start: 0.8683 (mtm) cc_final: 0.7886 (mtm) REVERT: A 925 ASN cc_start: 0.8411 (m-40) cc_final: 0.7979 (m-40) REVERT: A 957 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 1041 ASP cc_start: 0.7563 (t0) cc_final: 0.7171 (t0) REVERT: A 1110 TYR cc_start: 0.8863 (t80) cc_final: 0.8426 (t80) REVERT: D 581 VAL cc_start: 0.1778 (OUTLIER) cc_final: 0.1496 (m) REVERT: D 587 TYR cc_start: 0.0162 (t80) cc_final: -0.0575 (t80) REVERT: C 19 ARG cc_start: 0.5308 (ptp-170) cc_final: 0.4986 (mmp80) REVERT: C 177 MET cc_start: 0.3286 (tpp) cc_final: 0.2765 (ttp) REVERT: C 664 ILE cc_start: 0.8942 (mm) cc_final: 0.8685 (mm) REVERT: C 776 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8624 (ttpp) REVERT: C 994 ASP cc_start: 0.8224 (t70) cc_final: 0.7930 (t0) REVERT: C 1072 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7775 (mt-10) outliers start: 74 outliers final: 55 residues processed: 370 average time/residue: 0.1659 time to fit residues: 102.2706 Evaluate side-chains 365 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 194 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 310 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 125 optimal weight: 0.1980 chunk 279 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 159 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.139484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.112289 restraints weight = 99344.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.114297 restraints weight = 49016.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.116079 restraints weight = 29166.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116222 restraints weight = 20394.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.116436 restraints weight = 17752.527| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30486 Z= 0.103 Angle : 0.546 11.126 41480 Z= 0.278 Chirality : 0.043 0.214 4616 Planarity : 0.003 0.038 5375 Dihedral : 4.073 24.878 4050 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.79 % Allowed : 18.23 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.07 (0.14), residues: 3733 helix: 1.52 (0.17), residues: 1027 sheet: 0.00 (0.20), residues: 646 loop : -0.88 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 169 TYR 0.030 0.001 TYR B 396 PHE 0.021 0.001 PHE B 927 TRP 0.043 0.002 TRP D 168 HIS 0.012 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00231 (30444) covalent geometry : angle 0.54356 (41396) SS BOND : bond 0.00245 ( 42) SS BOND : angle 1.22463 ( 84) hydrogen bonds : bond 0.03343 ( 1130) hydrogen bonds : angle 4.64853 ( 3174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 1.151 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: B 176 LEU cc_start: 0.2170 (OUTLIER) cc_final: 0.1814 (pp) REVERT: B 191 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: B 195 LYS cc_start: 0.7631 (pptt) cc_final: 0.7150 (pttt) REVERT: B 223 LEU cc_start: 0.7963 (mp) cc_final: 0.7369 (mt) REVERT: B 297 SER cc_start: 0.8936 (m) cc_final: 0.8551 (p) REVERT: B 304 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8835 (tppt) REVERT: B 408 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4472 (tmm-80) REVERT: B 417 LYS cc_start: 0.3597 (tptt) cc_final: 0.3014 (ptmt) REVERT: B 508 TYR cc_start: 0.5496 (m-80) cc_final: 0.5160 (m-80) REVERT: B 592 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6689 (m-10) REVERT: B 752 LEU cc_start: 0.9619 (tp) cc_final: 0.9156 (tp) REVERT: B 957 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 983 ARG cc_start: 0.7997 (ttt180) cc_final: 0.7732 (ttt-90) REVERT: B 1030 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8724 (t) REVERT: A 177 MET cc_start: -0.0949 (mtt) cc_final: -0.2167 (mtt) REVERT: A 269 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.5286 (m-80) REVERT: A 664 ILE cc_start: 0.8911 (mm) cc_final: 0.8678 (mm) REVERT: A 780 GLU cc_start: 0.8267 (tt0) cc_final: 0.8064 (tt0) REVERT: A 900 MET cc_start: 0.8554 (mtm) cc_final: 0.7828 (mtm) REVERT: A 925 ASN cc_start: 0.8351 (m-40) cc_final: 0.7893 (m-40) REVERT: A 957 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 1041 ASP cc_start: 0.7567 (t0) cc_final: 0.7229 (t0) REVERT: A 1110 TYR cc_start: 0.8827 (t80) cc_final: 0.8389 (t80) REVERT: D 249 MET cc_start: 0.0075 (OUTLIER) cc_final: -0.0595 (ptt) REVERT: C 19 ARG cc_start: 0.5450 (ptp-170) cc_final: 0.5189 (mmp80) REVERT: C 88 ASP cc_start: 0.7459 (m-30) cc_final: 0.7258 (t0) REVERT: C 177 MET cc_start: 0.2996 (tpp) cc_final: 0.2615 (ttp) REVERT: C 664 ILE cc_start: 0.8913 (mm) cc_final: 0.8671 (mm) REVERT: C 726 ILE cc_start: 0.9132 (mp) cc_final: 0.8756 (mt) REVERT: C 764 ASN cc_start: 0.8157 (m-40) cc_final: 0.7877 (m110) REVERT: C 776 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8606 (ttpp) REVERT: C 994 ASP cc_start: 0.8091 (t70) cc_final: 0.7868 (t0) REVERT: C 1072 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7648 (mt-10) outliers start: 59 outliers final: 48 residues processed: 366 average time/residue: 0.1600 time to fit residues: 97.7161 Evaluate side-chains 363 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 312 optimal weight: 9.9990 chunk 141 optimal weight: 0.4980 chunk 171 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.138570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.111275 restraints weight = 100231.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113213 restraints weight = 48912.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.114658 restraints weight = 31946.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.115269 restraints weight = 22274.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.115677 restraints weight = 18571.559| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30486 Z= 0.119 Angle : 0.552 12.127 41480 Z= 0.281 Chirality : 0.043 0.215 4616 Planarity : 0.004 0.037 5375 Dihedral : 4.086 24.774 4050 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.91 % Allowed : 18.23 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3733 helix: 1.51 (0.17), residues: 1027 sheet: 0.02 (0.20), residues: 650 loop : -0.85 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.026 0.001 TYR A 265 PHE 0.024 0.001 PHE C 168 TRP 0.027 0.002 TRP C 886 HIS 0.012 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00274 (30444) covalent geometry : angle 0.55037 (41396) SS BOND : bond 0.00254 ( 42) SS BOND : angle 1.20259 ( 84) hydrogen bonds : bond 0.03410 ( 1130) hydrogen bonds : angle 4.65312 ( 3174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5558.07 seconds wall clock time: 96 minutes 41.23 seconds (5801.23 seconds total)