Starting phenix.real_space_refine on Wed Jun 25 21:49:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w98_32361/06_2025/7w98_32361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w98_32361/06_2025/7w98_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w98_32361/06_2025/7w98_32361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w98_32361/06_2025/7w98_32361.map" model { file = "/net/cci-nas-00/data/ceres_data/7w98_32361/06_2025/7w98_32361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w98_32361/06_2025/7w98_32361.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.099 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "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: 17.88, per 1000 atoms: 0.60 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: 7.63 Conformation dependent library (CDL) restraints added in 3.9 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: 4.49 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: 13.41 Time building geometry restraints manager: 8.95 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.390 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 70.890 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (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 TRP 0.005 0.001 TRP D 203 HIS 0.003 0.001 HIS C 49 PHE 0.011 0.001 PHE A 562 TYR 0.008 0.001 TYR B 873 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.27394 ( 1130) hydrogen bonds : angle 9.29155 ( 3174) SS BOND : bond 0.00279 ( 42) SS BOND : angle 0.81665 ( 84) covalent geometry : bond 0.00345 (30444) covalent geometry : angle 0.57393 (41396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 761 time to evaluate : 4.148 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 117 LEU cc_start: 0.7976 (mp) cc_final: 0.7630 (tp) REVERT: B 129 LYS cc_start: 0.8317 (mttt) cc_final: 0.8101 (mtpp) REVERT: B 143 VAL cc_start: 0.6342 (t) cc_final: 0.5748 (t) REVERT: B 458 LYS cc_start: 0.5962 (mppt) cc_final: 0.5163 (pttm) REVERT: B 708 SER cc_start: 0.7260 (t) cc_final: 0.6813 (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: 0.8091 (m-80) REVERT: B 859 THR cc_start: 0.7396 (m) cc_final: 0.7194 (t) REVERT: B 918 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7153 (mt-10) REVERT: B 1073 LYS cc_start: 0.8492 (mttt) cc_final: 0.8099 (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: 0.8447 (mt) REVERT: A 216 LEU cc_start: 0.6490 (mt) cc_final: 0.6262 (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: 0.5731 (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: 0.7961 (m-40) REVERT: A 752 LEU cc_start: 0.8921 (mt) cc_final: 0.8355 (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: 0.8271 (m-30) REVERT: A 984 LEU cc_start: 0.7725 (mp) cc_final: 0.6816 (mt) REVERT: D 32 PHE cc_start: 0.7028 (t80) cc_final: 0.6803 (t80) REVERT: D 323 MET cc_start: 0.4042 (mmt) cc_final: 0.3053 (mmt) REVERT: D 383 MET cc_start: 0.6514 (mtp) cc_final: 0.6309 (ppp) REVERT: D 557 MET cc_start: 0.3220 (ttp) cc_final: 0.2942 (ptm) REVERT: C 19 ARG cc_start: 0.6689 (ptp-170) cc_final: 0.6352 (tpm170) REVERT: C 55 PHE cc_start: 0.8153 (m-80) cc_final: 0.7415 (m-80) REVERT: C 86 PHE cc_start: 0.5868 (t80) cc_final: 0.5620 (t80) REVERT: C 104 TRP cc_start: 0.7976 (m-90) cc_final: 0.7300 (m100) REVERT: C 229 LEU cc_start: 0.8658 (mt) cc_final: 0.8446 (mt) REVERT: C 237 ARG cc_start: 0.6232 (mtm180) cc_final: 0.5734 (mpp80) REVERT: C 270 LEU cc_start: 0.8407 (mp) cc_final: 0.8149 (mp) REVERT: C 979 ASP cc_start: 0.8565 (m-30) cc_final: 0.8189 (m-30) REVERT: C 981 LEU cc_start: 0.8165 (tp) cc_final: 0.7952 (tp) REVERT: C 983 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7608 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 762 average time/residue: 0.5005 time to fit residues: 600.8416 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 : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.8980 chunk 285 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 460 ASN B 481 ASN B 907 ASN B 949 GLN B 955 ASN A 30 ASN A 66 HIS A 149 ASN A 165 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 764 ASN C 787 GLN C 935 GLN C1002 GLN C1083 HIS C1113 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.140425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.113107 restraints weight = 97900.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.115201 restraints weight = 48137.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.117037 restraints weight = 30231.405| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30486 Z= 0.225 Angle : 0.674 9.461 41480 Z= 0.354 Chirality : 0.047 0.212 4616 Planarity : 0.004 0.045 5375 Dihedral : 4.508 21.779 4050 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.42 % Allowed : 10.02 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3733 helix: 0.04 (0.16), residues: 997 sheet: -1.35 (0.18), residues: 677 loop : -1.53 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 477 HIS 0.007 0.001 HIS D 535 PHE 0.026 0.002 PHE A 592 TYR 0.023 0.002 TYR A 495 ARG 0.006 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 1130) hydrogen bonds : angle 5.93993 ( 3174) SS BOND : bond 0.00600 ( 42) SS BOND : angle 1.52320 ( 84) covalent geometry : bond 0.00509 (30444) covalent geometry : angle 0.67120 (41396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 436 time to evaluate : 3.209 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: B 128 ILE cc_start: 0.8568 (mp) cc_final: 0.8337 (mp) REVERT: B 195 LYS cc_start: 0.7458 (pptt) cc_final: 0.6566 (pttt) REVERT: B 286 THR cc_start: 0.8842 (p) cc_final: 0.8528 (t) REVERT: B 408 ARG cc_start: 0.4328 (OUTLIER) cc_final: 0.3949 (tmm-80) REVERT: B 752 LEU cc_start: 0.9387 (mp) cc_final: 0.8992 (tp) REVERT: B 756 TYR cc_start: 0.9085 (m-80) cc_final: 0.8615 (m-80) REVERT: B 870 ILE cc_start: 0.9219 (mm) cc_final: 0.8881 (mt) REVERT: B 900 MET cc_start: 0.8468 (mmt) cc_final: 0.7567 (mpp) REVERT: B 976 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 983 ARG cc_start: 0.7756 (ttt180) cc_final: 0.7362 (mtp180) REVERT: B 1030 SER cc_start: 0.9161 (m) cc_final: 0.8767 (t) REVERT: B 1114 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 177 MET cc_start: 0.0833 (mmt) cc_final: -0.0105 (mmt) REVERT: A 265 TYR cc_start: 0.7090 (p90) cc_final: 0.6491 (p90) REVERT: A 552 LEU cc_start: 0.8677 (mm) cc_final: 0.8369 (mm) REVERT: A 751 ASN cc_start: 0.8907 (m-40) cc_final: 0.8583 (m-40) REVERT: A 755 GLN cc_start: 0.7951 (mp10) cc_final: 0.7717 (mp10) REVERT: A 907 ASN cc_start: 0.9133 (t0) cc_final: 0.8753 (t0) REVERT: A 979 ASP cc_start: 0.8814 (m-30) cc_final: 0.8305 (m-30) REVERT: A 981 LEU cc_start: 0.9069 (tp) cc_final: 0.8845 (tt) REVERT: A 1031 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 1041 ASP cc_start: 0.7392 (t0) cc_final: 0.6970 (t0) REVERT: A 1110 TYR cc_start: 0.8708 (t80) cc_final: 0.8411 (t80) REVERT: D 190 MET cc_start: -0.1202 (tpp) cc_final: -0.1411 (tpp) REVERT: D 202 TYR cc_start: 0.6240 (t80) cc_final: 0.5843 (m-80) REVERT: D 582 ARG cc_start: 0.6811 (mpt180) cc_final: 0.5424 (mmp-170) REVERT: C 19 ARG cc_start: 0.6535 (ptp-170) cc_final: 0.6054 (tpt170) REVERT: C 55 PHE cc_start: 0.7714 (m-80) cc_final: 0.7202 (m-80) REVERT: C 177 MET cc_start: 0.2400 (tpp) cc_final: 0.2160 (tpp) REVERT: C 390 LEU cc_start: 0.6821 (mp) cc_final: 0.6058 (mt) REVERT: C 979 ASP cc_start: 0.8621 (m-30) cc_final: 0.8281 (m-30) REVERT: C 983 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: C 994 ASP cc_start: 0.8266 (t70) cc_final: 0.7871 (t0) outliers start: 80 outliers final: 47 residues processed: 490 average time/residue: 0.4058 time to fit residues: 319.8654 Evaluate side-chains 371 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 321 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 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 976 VAL 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 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 226 LEU Chi-restraints excluded: chain A residue 306 PHE 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 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 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 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 587 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 316 optimal weight: 7.9990 chunk 370 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 356 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 273 optimal weight: 6.9990 chunk 202 optimal weight: 0.0970 overall best weight: 1.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 764 ASN A 703 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 655 HIS C 764 ASN C 914 ASN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.138820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.110485 restraints weight = 99859.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.112692 restraints weight = 49070.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114121 restraints weight = 29293.680| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30486 Z= 0.187 Angle : 0.605 10.887 41480 Z= 0.317 Chirality : 0.045 0.313 4616 Planarity : 0.004 0.050 5375 Dihedral : 4.392 22.248 4050 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.15 % Allowed : 12.48 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3733 helix: 0.73 (0.16), residues: 1020 sheet: -0.89 (0.19), residues: 673 loop : -1.38 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 64 HIS 0.004 0.001 HIS B 66 PHE 0.031 0.002 PHE B 392 TYR 0.018 0.002 TYR C 421 ARG 0.006 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 1130) hydrogen bonds : angle 5.54127 ( 3174) SS BOND : bond 0.00577 ( 42) SS BOND : angle 1.40062 ( 84) covalent geometry : bond 0.00426 (30444) covalent geometry : angle 0.60188 (41396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 377 time to evaluate : 4.262 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 63 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6698 (t) REVERT: B 126 VAL cc_start: 0.8327 (t) cc_final: 0.8056 (t) REVERT: B 195 LYS cc_start: 0.7731 (pptt) cc_final: 0.6659 (pttt) REVERT: B 223 LEU cc_start: 0.8048 (mp) cc_final: 0.7481 (mt) REVERT: B 286 THR cc_start: 0.8774 (p) cc_final: 0.8392 (t) REVERT: B 297 SER cc_start: 0.8897 (m) cc_final: 0.8577 (p) REVERT: B 592 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: B 756 TYR cc_start: 0.9021 (m-80) cc_final: 0.8802 (m-80) REVERT: B 900 MET cc_start: 0.8617 (mmt) cc_final: 0.8110 (mpp) REVERT: B 957 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7495 (tm-30) REVERT: B 1030 SER cc_start: 0.9030 (m) cc_final: 0.8749 (t) REVERT: A 177 MET cc_start: 0.0521 (mmt) cc_final: -0.0136 (mmt) REVERT: A 231 ILE cc_start: 0.8406 (mt) cc_final: 0.8202 (mt) REVERT: A 338 PHE cc_start: 0.7227 (m-80) cc_final: 0.6931 (m-80) REVERT: A 552 LEU cc_start: 0.8658 (mm) cc_final: 0.8282 (mm) REVERT: A 751 ASN cc_start: 0.8963 (m-40) cc_final: 0.8689 (m-40) REVERT: A 787 GLN cc_start: 0.8147 (pm20) cc_final: 0.7735 (pm20) REVERT: A 957 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 979 ASP cc_start: 0.8805 (m-30) cc_final: 0.8383 (m-30) REVERT: A 1031 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7918 (mt-10) REVERT: A 1041 ASP cc_start: 0.7327 (t0) cc_final: 0.7009 (t0) REVERT: D 239 HIS cc_start: 0.3471 (m-70) cc_final: 0.3074 (m170) REVERT: D 480 MET cc_start: 0.3212 (mtt) cc_final: 0.3003 (mtp) REVERT: D 613 TYR cc_start: 0.1481 (p90) cc_final: 0.0774 (p90) REVERT: C 19 ARG cc_start: 0.6270 (ptp-170) cc_final: 0.5841 (tpt170) REVERT: C 55 PHE cc_start: 0.7568 (m-80) cc_final: 0.6920 (m-80) REVERT: C 664 ILE cc_start: 0.8962 (mm) cc_final: 0.8647 (mm) REVERT: C 776 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8557 (ttpp) REVERT: C 979 ASP cc_start: 0.8310 (m-30) cc_final: 0.8062 (m-30) REVERT: C 994 ASP cc_start: 0.8267 (t70) cc_final: 0.7797 (t0) REVERT: C 1019 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8376 (ttp80) REVERT: C 1072 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8021 (mt-10) outliers start: 104 outliers final: 57 residues processed: 455 average time/residue: 0.4158 time to fit residues: 313.7731 Evaluate side-chains 374 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 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 515 PHE 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 875 SER 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 1061 VAL Chi-restraints excluded: chain B residue 1081 ILE 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 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 226 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 912 THR 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 994 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain D residue 364 VAL 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 91 TYR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE 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 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 712 ILE 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 991 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 278 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 0.0000 chunk 27 optimal weight: 2.9990 chunk 253 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 703 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 950 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN C 955 ASN C 957 GLN C1036 GLN 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 = 0.138440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.110529 restraints weight = 99895.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.112590 restraints weight = 48753.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.113968 restraints weight = 29315.781| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30486 Z= 0.158 Angle : 0.573 10.001 41480 Z= 0.297 Chirality : 0.044 0.176 4616 Planarity : 0.004 0.044 5375 Dihedral : 4.358 21.231 4050 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.24 % Allowed : 14.08 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 3733 helix: 1.12 (0.17), residues: 1004 sheet: -0.61 (0.19), residues: 650 loop : -1.22 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 275 HIS 0.004 0.001 HIS D 239 PHE 0.019 0.002 PHE B 32 TYR 0.019 0.002 TYR B 144 ARG 0.007 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1130) hydrogen bonds : angle 5.27792 ( 3174) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.37991 ( 84) covalent geometry : bond 0.00361 (30444) covalent geometry : angle 0.57047 (41396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 366 time to evaluate : 3.651 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 126 VAL cc_start: 0.8269 (t) cc_final: 0.8023 (t) REVERT: B 223 LEU cc_start: 0.7925 (mp) cc_final: 0.6639 (mt) REVERT: B 297 SER cc_start: 0.8977 (m) cc_final: 0.8634 (p) REVERT: B 304 LYS cc_start: 0.8686 (mppt) cc_final: 0.8442 (mppt) REVERT: B 403 ARG cc_start: 0.4256 (mtm180) cc_final: 0.3987 (mtp85) REVERT: B 408 ARG cc_start: 0.4365 (OUTLIER) cc_final: 0.3930 (tmm-80) REVERT: B 752 LEU cc_start: 0.9547 (tp) cc_final: 0.9023 (tp) REVERT: B 900 MET cc_start: 0.8628 (mmt) cc_final: 0.7821 (mpp) REVERT: B 957 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 177 MET cc_start: -0.0548 (mmt) cc_final: -0.0849 (mmt) REVERT: A 231 ILE cc_start: 0.8376 (mt) cc_final: 0.8124 (mt) REVERT: A 265 TYR cc_start: 0.7009 (p90) cc_final: 0.6628 (p90) REVERT: A 269 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.5145 (m-80) REVERT: A 338 PHE cc_start: 0.7240 (m-80) cc_final: 0.6877 (m-80) REVERT: A 368 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7590 (mt) REVERT: A 552 LEU cc_start: 0.8653 (mm) cc_final: 0.8306 (mm) REVERT: A 787 GLN cc_start: 0.8186 (pm20) cc_final: 0.7822 (pm20) REVERT: A 925 ASN cc_start: 0.8389 (m-40) cc_final: 0.7949 (m-40) REVERT: A 957 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 1041 ASP cc_start: 0.7568 (t0) cc_final: 0.7068 (t0) REVERT: A 1110 TYR cc_start: 0.8863 (t80) cc_final: 0.8464 (t80) REVERT: D 249 MET cc_start: 0.0900 (ttp) cc_final: 0.0517 (ptt) REVERT: D 474 MET cc_start: -0.0357 (tpt) cc_final: -0.0723 (tpt) REVERT: D 587 TYR cc_start: 0.0191 (t80) cc_final: -0.0526 (t80) REVERT: C 19 ARG cc_start: 0.6049 (ptp-170) cc_final: 0.5594 (tpt170) REVERT: C 92 PHE cc_start: 0.6881 (t80) cc_final: 0.6679 (t80) REVERT: C 177 MET cc_start: 0.2743 (tpp) cc_final: 0.2414 (ttp) REVERT: C 664 ILE cc_start: 0.8960 (mm) cc_final: 0.8312 (mm) REVERT: C 776 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8535 (ttpp) REVERT: C 979 ASP cc_start: 0.8334 (m-30) cc_final: 0.8077 (m-30) REVERT: C 994 ASP cc_start: 0.8232 (t70) cc_final: 0.7970 (t0) REVERT: C 1072 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7961 (mt-10) outliers start: 107 outliers final: 64 residues processed: 447 average time/residue: 0.3989 time to fit residues: 290.7589 Evaluate side-chains 376 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 308 time to evaluate : 3.332 ------------------------------------------------------------------------------- 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 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 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 515 PHE 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 937 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 997 ILE 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 95 THR Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 PHE 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 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 855 PHE Chi-restraints excluded: chain A residue 911 VAL 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 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 D residue 504 PHE 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 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 599 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 719 THR 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 991 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 36 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 272 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 919 ASN A 165 ASN A 703 ASN A 751 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 950 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.136487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.109124 restraints weight = 96902.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.111348 restraints weight = 48387.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.112678 restraints weight = 29339.731| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5702 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= 0.175 Angle : 0.598 10.913 41480 Z= 0.309 Chirality : 0.045 0.191 4616 Planarity : 0.004 0.041 5375 Dihedral : 4.552 27.229 4050 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.30 % Allowed : 15.35 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3733 helix: 1.07 (0.17), residues: 1015 sheet: -0.55 (0.19), residues: 668 loop : -1.20 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 104 HIS 0.004 0.001 HIS B 146 PHE 0.019 0.002 PHE A 133 TYR 0.019 0.002 TYR C 269 ARG 0.006 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 1130) hydrogen bonds : angle 5.24716 ( 3174) SS BOND : bond 0.00406 ( 42) SS BOND : angle 1.15483 ( 84) covalent geometry : bond 0.00400 (30444) covalent geometry : angle 0.59586 (41396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 344 time to evaluate : 3.627 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 223 LEU cc_start: 0.7734 (mp) cc_final: 0.7098 (mt) REVERT: B 297 SER cc_start: 0.8951 (m) cc_final: 0.8595 (p) REVERT: B 304 LYS cc_start: 0.8662 (mppt) cc_final: 0.8369 (mppt) REVERT: B 408 ARG cc_start: 0.4401 (OUTLIER) cc_final: 0.4086 (tmm-80) REVERT: B 900 MET cc_start: 0.8687 (mmt) cc_final: 0.7898 (mpp) REVERT: B 957 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 231 ILE cc_start: 0.8367 (mt) cc_final: 0.8132 (mt) REVERT: A 265 TYR cc_start: 0.6999 (p90) cc_final: 0.6669 (p90) REVERT: A 269 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5129 (m-80) REVERT: A 756 TYR cc_start: 0.8984 (m-80) cc_final: 0.8651 (m-10) REVERT: A 925 ASN cc_start: 0.8407 (m-40) cc_final: 0.8010 (m-40) REVERT: A 957 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 1110 TYR cc_start: 0.8878 (t80) cc_final: 0.8459 (t80) REVERT: D 45 LEU cc_start: 0.7954 (mt) cc_final: 0.7700 (mp) REVERT: D 72 PHE cc_start: 0.5302 (OUTLIER) cc_final: 0.4952 (t80) REVERT: D 239 HIS cc_start: 0.3299 (m-70) cc_final: 0.3074 (m170) REVERT: D 247 LYS cc_start: -0.0455 (mmtt) cc_final: -0.0744 (mmtm) REVERT: D 581 VAL cc_start: 0.2085 (OUTLIER) cc_final: 0.1815 (m) REVERT: D 587 TYR cc_start: 0.0279 (t80) cc_final: -0.0417 (t80) REVERT: C 19 ARG cc_start: 0.5844 (ptp-170) cc_final: 0.5451 (tpt170) REVERT: C 104 TRP cc_start: 0.8377 (m100) cc_final: 0.8169 (m100) REVERT: C 177 MET cc_start: 0.3089 (tpp) cc_final: 0.2573 (ttp) REVERT: C 180 GLU cc_start: -0.1975 (OUTLIER) cc_final: -0.2694 (tp30) REVERT: C 390 LEU cc_start: 0.8001 (mp) cc_final: 0.7181 (tp) REVERT: C 776 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8537 (ttpp) REVERT: C 796 ASP cc_start: 0.8023 (t0) cc_final: 0.7752 (t0) REVERT: C 976 VAL cc_start: 0.8516 (t) cc_final: 0.8206 (p) REVERT: C 994 ASP cc_start: 0.8327 (t70) cc_final: 0.8028 (t0) REVERT: C 1072 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7943 (mt-10) outliers start: 109 outliers final: 75 residues processed: 425 average time/residue: 0.3850 time to fit residues: 272.3847 Evaluate side-chains 390 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 309 time to evaluate : 3.386 ------------------------------------------------------------------------------- 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 240 THR 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 402 ILE 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 734 THR 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 1061 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 99 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 PHE 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 299 THR Chi-restraints excluded: chain A residue 306 PHE 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 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 855 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 914 ASN 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 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain D residue 72 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 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 GLU 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 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL 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 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 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE 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 237 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 350 optimal weight: 3.9990 chunk 366 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 275 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 422 ASN B 655 HIS B 907 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN D 397 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN C 164 ASN C 450 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.133459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.105704 restraints weight = 101187.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.107816 restraints weight = 50435.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.109080 restraints weight = 30724.236| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 30486 Z= 0.252 Angle : 0.681 10.514 41480 Z= 0.354 Chirality : 0.047 0.186 4616 Planarity : 0.004 0.041 5375 Dihedral : 5.026 27.490 4050 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.82 % Allowed : 16.44 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 3733 helix: 0.80 (0.17), residues: 1016 sheet: -0.60 (0.20), residues: 644 loop : -1.39 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 461 HIS 0.018 0.002 HIS B 245 PHE 0.031 0.002 PHE A 79 TYR 0.021 0.002 TYR C 904 ARG 0.007 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 1130) hydrogen bonds : angle 5.51582 ( 3174) SS BOND : bond 0.00437 ( 42) SS BOND : angle 1.33993 ( 84) covalent geometry : bond 0.00577 (30444) covalent geometry : angle 0.67928 (41396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 320 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 LEU cc_start: 0.1783 (OUTLIER) cc_final: 0.1527 (pp) REVERT: B 223 LEU cc_start: 0.8086 (mp) cc_final: 0.7488 (mt) REVERT: B 297 SER cc_start: 0.8991 (m) cc_final: 0.8533 (t) REVERT: B 304 LYS cc_start: 0.8778 (mppt) cc_final: 0.8458 (mppt) REVERT: B 900 MET cc_start: 0.8728 (mmt) cc_final: 0.8437 (mpp) REVERT: B 957 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 178 ASP cc_start: 0.5731 (p0) cc_final: 0.4718 (p0) REVERT: A 265 TYR cc_start: 0.6991 (p90) cc_final: 0.6783 (p90) REVERT: A 269 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.5331 (m-80) REVERT: A 703 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8396 (t0) REVERT: A 856 ASN cc_start: 0.8493 (t0) cc_final: 0.8195 (m110) REVERT: A 925 ASN cc_start: 0.8518 (m-40) cc_final: 0.8194 (m-40) REVERT: A 957 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 1110 TYR cc_start: 0.8905 (t80) cc_final: 0.8497 (t80) REVERT: D 72 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.5067 (t80) REVERT: D 332 MET cc_start: 0.1884 (ptm) cc_final: 0.1674 (ppp) REVERT: D 587 TYR cc_start: 0.0421 (t80) cc_final: -0.0231 (t80) REVERT: C 19 ARG cc_start: 0.5661 (ptp-170) cc_final: 0.5381 (tpm170) REVERT: C 177 MET cc_start: 0.3257 (tpp) cc_final: 0.2982 (ttp) REVERT: C 180 GLU cc_start: -0.1081 (OUTLIER) cc_final: -0.2310 (tp30) REVERT: C 390 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7278 (tp) REVERT: C 664 ILE cc_start: 0.8860 (mm) cc_final: 0.8653 (mm) REVERT: C 776 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8625 (ttpp) REVERT: C 979 ASP cc_start: 0.8373 (m-30) cc_final: 0.8130 (m-30) REVERT: C 994 ASP cc_start: 0.8431 (t70) cc_final: 0.7940 (t0) REVERT: C 1072 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (mt-10) outliers start: 126 outliers final: 86 residues processed: 414 average time/residue: 0.3824 time to fit residues: 262.4880 Evaluate side-chains 386 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 293 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 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 270 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 402 ILE 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 734 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 997 ILE 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 95 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 552 LEU 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 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN 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 994 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 72 PHE 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 180 GLU 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 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 309 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 369 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 511 VAL 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 708 SER Chi-restraints excluded: chain C residue 712 ILE 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 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 129 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 245 HIS A 317 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 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.137338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109642 restraints weight = 99776.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.111891 restraints weight = 49291.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.113280 restraints weight = 29442.372| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 : 0.003 0.039 30486 Z= 0.121 Angle : 0.560 9.479 41480 Z= 0.289 Chirality : 0.043 0.195 4616 Planarity : 0.004 0.041 5375 Dihedral : 4.446 26.415 4050 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.63 % Allowed : 17.93 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3733 helix: 1.21 (0.17), residues: 1014 sheet: -0.49 (0.20), residues: 637 loop : -1.22 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.003 0.001 HIS D 374 PHE 0.023 0.001 PHE D 315 TYR 0.021 0.001 TYR D 237 ARG 0.009 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1130) hydrogen bonds : angle 5.01873 ( 3174) SS BOND : bond 0.00287 ( 42) SS BOND : angle 1.04579 ( 84) covalent geometry : bond 0.00273 (30444) covalent geometry : angle 0.55880 (41396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 350 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 ILE cc_start: 0.8477 (mm) cc_final: 0.8232 (tp) REVERT: B 176 LEU cc_start: 0.2701 (OUTLIER) cc_final: 0.2336 (pp) REVERT: B 195 LYS cc_start: 0.7617 (pptt) cc_final: 0.6931 (ptpt) REVERT: B 223 LEU cc_start: 0.8033 (mp) cc_final: 0.7442 (mt) REVERT: B 297 SER cc_start: 0.8920 (m) cc_final: 0.8529 (p) REVERT: B 408 ARG cc_start: 0.4570 (OUTLIER) cc_final: 0.4106 (tmm-80) REVERT: B 752 LEU cc_start: 0.9623 (tp) cc_final: 0.9191 (tp) REVERT: B 957 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 36 VAL cc_start: 0.8633 (t) cc_final: 0.8390 (p) REVERT: A 191 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 265 TYR cc_start: 0.6929 (p90) cc_final: 0.6703 (p90) REVERT: A 269 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: A 703 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8494 (t0) REVERT: A 856 ASN cc_start: 0.8420 (t0) cc_final: 0.8096 (m110) REVERT: A 925 ASN cc_start: 0.8397 (m-40) cc_final: 0.8014 (m-40) REVERT: A 957 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 1110 TYR cc_start: 0.8859 (t80) cc_final: 0.8453 (t80) REVERT: D 72 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.5151 (t80) REVERT: D 270 MET cc_start: 0.0918 (mpp) cc_final: 0.0531 (mpp) REVERT: D 581 VAL cc_start: 0.1638 (OUTLIER) cc_final: 0.1344 (m) REVERT: D 587 TYR cc_start: 0.0168 (t80) cc_final: -0.0504 (t80) REVERT: C 177 MET cc_start: 0.3146 (tpp) cc_final: 0.2751 (ttp) REVERT: C 274 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 390 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7434 (tp) REVERT: C 611 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8891 (tt) REVERT: C 776 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8627 (ttpp) REVERT: C 979 ASP cc_start: 0.8329 (m-30) cc_final: 0.8065 (m-30) REVERT: C 994 ASP cc_start: 0.8229 (t70) cc_final: 0.7966 (t0) REVERT: C 1072 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7754 (mt-10) outliers start: 87 outliers final: 54 residues processed: 414 average time/residue: 0.3805 time to fit residues: 263.8998 Evaluate side-chains 371 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 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 599 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1004 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 95 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS 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 299 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 392 PHE 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 573 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL 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 390 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 151 optimal weight: 0.0010 chunk 159 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 335 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.6590 ------------------------------------------------------------------------------- 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 245 HIS ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN C 69 HIS C 125 ASN C 764 ASN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.135520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.108047 restraints weight = 100111.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.110177 restraints weight = 49711.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.111427 restraints weight = 30174.497| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30486 Z= 0.160 Angle : 0.595 10.264 41480 Z= 0.306 Chirality : 0.044 0.227 4616 Planarity : 0.004 0.040 5375 Dihedral : 4.539 26.071 4050 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.85 % Allowed : 18.72 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3733 helix: 1.13 (0.17), residues: 1022 sheet: -0.50 (0.20), residues: 653 loop : -1.22 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS D 378 PHE 0.024 0.002 PHE D 315 TYR 0.026 0.002 TYR C 904 ARG 0.007 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1130) hydrogen bonds : angle 5.07436 ( 3174) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.47257 ( 84) covalent geometry : bond 0.00368 (30444) covalent geometry : angle 0.59236 (41396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 323 time to evaluate : 3.695 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: B 119 ILE cc_start: 0.8426 (mm) cc_final: 0.8084 (tt) REVERT: B 176 LEU cc_start: 0.2566 (OUTLIER) cc_final: 0.2170 (pp) REVERT: B 191 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: B 195 LYS cc_start: 0.7680 (pptt) cc_final: 0.7000 (ptpt) REVERT: B 223 LEU cc_start: 0.8117 (mp) cc_final: 0.7442 (mt) REVERT: B 297 SER cc_start: 0.8987 (m) cc_final: 0.8527 (t) REVERT: B 304 LYS cc_start: 0.8699 (mppt) cc_final: 0.8380 (mppt) REVERT: B 408 ARG cc_start: 0.4473 (OUTLIER) cc_final: 0.4084 (tmm-80) REVERT: B 458 LYS cc_start: 0.6447 (mptt) cc_final: 0.5498 (pttm) REVERT: B 957 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 269 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.5267 (m-80) REVERT: A 703 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8408 (t0) REVERT: A 856 ASN cc_start: 0.8504 (t0) cc_final: 0.8214 (m110) REVERT: A 925 ASN cc_start: 0.8435 (m-40) cc_final: 0.8084 (m-40) REVERT: A 957 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 1110 TYR cc_start: 0.8875 (t80) cc_final: 0.8465 (t80) REVERT: D 72 PHE cc_start: 0.5524 (OUTLIER) cc_final: 0.5170 (t80) REVERT: D 270 MET cc_start: 0.1389 (mpp) cc_final: 0.0945 (mpp) REVERT: D 587 TYR cc_start: 0.0178 (t80) cc_final: -0.0468 (t80) REVERT: C 177 MET cc_start: 0.3318 (tpp) cc_final: 0.2883 (ttp) REVERT: C 390 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7415 (tp) REVERT: C 776 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8646 (ttpp) REVERT: C 979 ASP cc_start: 0.8308 (m-30) cc_final: 0.7986 (m-30) REVERT: C 994 ASP cc_start: 0.8314 (t70) cc_final: 0.8010 (t0) REVERT: C 1072 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: C 1107 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7098 (ttt90) outliers start: 94 outliers final: 77 residues processed: 391 average time/residue: 0.3820 time to fit residues: 249.2939 Evaluate side-chains 390 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 304 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 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 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 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1004 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 95 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS 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 299 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 429 PHE 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 573 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN 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 D residue 32 PHE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 120 VAL 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 298 GLU Chi-restraints excluded: chain C residue 309 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 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 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 587 ILE 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 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 77 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 85 optimal weight: 0.0050 chunk 189 optimal weight: 3.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 245 HIS ** B 540 ASN ** 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.136842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109335 restraints weight = 100549.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.111559 restraints weight = 49726.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112657 restraints weight = 29865.971| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30486 Z= 0.129 Angle : 0.574 10.157 41480 Z= 0.294 Chirality : 0.043 0.212 4616 Planarity : 0.004 0.040 5375 Dihedral : 4.412 25.473 4050 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.70 % Allowed : 19.05 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3733 helix: 1.19 (0.17), residues: 1027 sheet: -0.42 (0.20), residues: 661 loop : -1.14 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 886 HIS 0.003 0.001 HIS D 374 PHE 0.023 0.001 PHE A 486 TYR 0.025 0.001 TYR A 265 ARG 0.006 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1130) hydrogen bonds : angle 4.97683 ( 3174) SS BOND : bond 0.00301 ( 42) SS BOND : angle 1.17215 ( 84) covalent geometry : bond 0.00295 (30444) covalent geometry : angle 0.57221 (41396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 321 time to evaluate : 3.603 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: B 119 ILE cc_start: 0.8403 (mm) cc_final: 0.8129 (tt) REVERT: B 176 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.2133 (pp) REVERT: B 191 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: B 195 LYS cc_start: 0.7661 (pptt) cc_final: 0.7028 (ptpt) REVERT: B 223 LEU cc_start: 0.7926 (mp) cc_final: 0.7228 (mt) REVERT: B 297 SER cc_start: 0.8970 (m) cc_final: 0.8576 (p) REVERT: B 408 ARG cc_start: 0.4542 (OUTLIER) cc_final: 0.4026 (tmm-80) REVERT: B 417 LYS cc_start: 0.3403 (OUTLIER) cc_final: 0.3193 (mmtt) REVERT: B 752 LEU cc_start: 0.9657 (tp) cc_final: 0.9278 (tp) REVERT: B 900 MET cc_start: 0.8705 (mmt) cc_final: 0.8147 (mpp) REVERT: B 957 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 269 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: A 319 ARG cc_start: 0.7311 (tpp80) cc_final: 0.7074 (tpp80) REVERT: A 703 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8396 (t0) REVERT: A 856 ASN cc_start: 0.8475 (t0) cc_final: 0.8140 (m110) REVERT: A 925 ASN cc_start: 0.8429 (m-40) cc_final: 0.8080 (m-40) REVERT: A 957 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 1110 TYR cc_start: 0.8864 (t80) cc_final: 0.8456 (t80) REVERT: D 72 PHE cc_start: 0.5524 (OUTLIER) cc_final: 0.5176 (t80) REVERT: D 270 MET cc_start: 0.1819 (mpp) cc_final: 0.1307 (mpp) REVERT: D 587 TYR cc_start: 0.0245 (t80) cc_final: -0.0404 (t80) REVERT: C 177 MET cc_start: 0.3074 (tpp) cc_final: 0.2723 (ttp) REVERT: C 390 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7755 (tp) REVERT: C 611 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8898 (tt) REVERT: C 776 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8652 (ttpp) REVERT: C 976 VAL cc_start: 0.8798 (t) cc_final: 0.8029 (p) REVERT: C 979 ASP cc_start: 0.8429 (m-30) cc_final: 0.7726 (m-30) REVERT: C 994 ASP cc_start: 0.8236 (t70) cc_final: 0.7963 (t0) REVERT: C 1072 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7815 (mt-10) outliers start: 89 outliers final: 68 residues processed: 389 average time/residue: 0.4025 time to fit residues: 262.0051 Evaluate side-chains 380 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 302 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 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 245 HIS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 417 LYS 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 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1004 LEU 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 119 ILE Chi-restraints excluded: chain A residue 131 CYS 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 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 429 PHE 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 573 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 855 PHE 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 72 PHE Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 572 ASN 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 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 730 SER 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 991 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 266 optimal weight: 0.3980 chunk 287 optimal weight: 0.4980 chunk 261 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 107 optimal weight: 0.0270 chunk 151 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 245 HIS ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN C 764 ASN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.137800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.110385 restraints weight = 99962.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.112637 restraints weight = 49795.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.113938 restraints weight = 29989.445| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30486 Z= 0.114 Angle : 0.570 15.172 41480 Z= 0.289 Chirality : 0.043 0.253 4616 Planarity : 0.004 0.043 5375 Dihedral : 4.272 24.998 4050 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.45 % Allowed : 19.69 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3733 helix: 1.31 (0.17), residues: 1027 sheet: -0.23 (0.19), residues: 665 loop : -1.11 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 48 HIS 0.008 0.001 HIS B 245 PHE 0.025 0.001 PHE A 486 TYR 0.025 0.001 TYR A 265 ARG 0.006 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 1130) hydrogen bonds : angle 4.85693 ( 3174) SS BOND : bond 0.00276 ( 42) SS BOND : angle 1.07187 ( 84) covalent geometry : bond 0.00258 (30444) covalent geometry : angle 0.56824 (41396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 324 time to evaluate : 4.322 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: B 176 LEU cc_start: 0.2880 (OUTLIER) cc_final: 0.2453 (pp) REVERT: B 191 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: B 195 LYS cc_start: 0.7664 (pptt) cc_final: 0.7060 (ptpt) REVERT: B 223 LEU cc_start: 0.7920 (mp) cc_final: 0.7270 (mt) REVERT: B 297 SER cc_start: 0.8911 (m) cc_final: 0.8503 (p) REVERT: B 408 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4261 (tmm-80) REVERT: B 508 TYR cc_start: 0.5663 (m-80) cc_final: 0.5381 (m-80) REVERT: B 752 LEU cc_start: 0.9658 (tp) cc_final: 0.9275 (tp) REVERT: B 900 MET cc_start: 0.8684 (mmt) cc_final: 0.8139 (mpp) REVERT: B 957 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 269 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: A 319 ARG cc_start: 0.7465 (tpp80) cc_final: 0.7233 (tpp80) REVERT: A 703 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8425 (t0) REVERT: A 856 ASN cc_start: 0.8468 (t0) cc_final: 0.8104 (m110) REVERT: A 925 ASN cc_start: 0.8429 (m-40) cc_final: 0.8057 (m-40) REVERT: A 957 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7603 (tm-30) REVERT: A 1110 TYR cc_start: 0.8846 (t80) cc_final: 0.8444 (t80) REVERT: D 72 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.5171 (t80) REVERT: D 270 MET cc_start: 0.1786 (mpp) cc_final: -0.0393 (tpp) REVERT: D 572 ASN cc_start: 0.4553 (OUTLIER) cc_final: 0.3809 (p0) REVERT: D 587 TYR cc_start: 0.0166 (t80) cc_final: -0.0557 (t80) REVERT: C 177 MET cc_start: 0.3124 (tpp) cc_final: 0.2767 (ttp) REVERT: C 390 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7617 (tp) REVERT: C 611 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8888 (tt) REVERT: C 776 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8657 (ttpp) REVERT: C 976 VAL cc_start: 0.8789 (t) cc_final: 0.8056 (p) REVERT: C 979 ASP cc_start: 0.8438 (m-30) cc_final: 0.7752 (m-30) REVERT: C 990 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: C 994 ASP cc_start: 0.8173 (t70) cc_final: 0.7892 (t0) REVERT: C 1072 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7815 (mt-10) outliers start: 81 outliers final: 62 residues processed: 386 average time/residue: 0.4526 time to fit residues: 292.6165 Evaluate side-chains 377 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 304 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 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 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 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1004 LEU 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 119 ILE Chi-restraints excluded: chain A residue 131 CYS 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 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 429 PHE 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 573 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 855 PHE 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 72 PHE Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU 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 611 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 704 SER 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 991 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 366 optimal weight: 0.0570 chunk 292 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 376 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 350 optimal weight: 0.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 245 HIS ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN A 762 GLN A 914 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN C 764 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.135684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.109362 restraints weight = 97432.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.111069 restraints weight = 50011.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113128 restraints weight = 29751.671| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30486 Z= 0.157 Angle : 0.603 13.604 41480 Z= 0.307 Chirality : 0.044 0.254 4616 Planarity : 0.004 0.040 5375 Dihedral : 4.434 25.286 4050 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.63 % Allowed : 19.56 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3733 helix: 1.25 (0.17), residues: 1028 sheet: -0.31 (0.20), residues: 648 loop : -1.14 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 48 HIS 0.006 0.001 HIS B 245 PHE 0.026 0.002 PHE C 168 TYR 0.024 0.002 TYR A 265 ARG 0.006 0.001 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 1130) hydrogen bonds : angle 4.96456 ( 3174) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.12889 ( 84) covalent geometry : bond 0.00363 (30444) covalent geometry : angle 0.60117 (41396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12475.13 seconds wall clock time: 220 minutes 40.59 seconds (13240.59 seconds total)