Starting phenix.real_space_refine on Fri Mar 6 09:25:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9b_32363/03_2026/7w9b_32363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9b_32363/03_2026/7w9b_32363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9b_32363/03_2026/7w9b_32363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9b_32363/03_2026/7w9b_32363.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9b_32363/03_2026/7w9b_32363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9b_32363/03_2026/7w9b_32363.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.111 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 226 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "D" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Time building chain proxies: 6.01, per 1000 atoms: 0.20 Number of scatterers: 29737 At special positions: 0 Unit cell: (156.299, 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 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: 95 helices and 49 sheets defined 30.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 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 365 through 370 removed outlier: 3.733A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.440A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.512A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.891A 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 783 removed outlier: 3.556A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.843A 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 removed outlier: 3.526A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.802A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.532A 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: 3.679A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (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: 3.776A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.833A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.733A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.623A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A 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: 3.571A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.727A 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 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.711A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.618A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.568A 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: 4.552A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.679A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.887A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.287A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.645A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.561A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.533A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix removed outlier: 3.715A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.736A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.001A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.607A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.945A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.521A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.923A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.524A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.608A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.052A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.718A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.824A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.518A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.607A pdb=" N ASN A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.875A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.141A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.818A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 4.463A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.766A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.546A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.761A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.596A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 780 removed outlier: 3.512A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 773 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.642A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.541A pdb=" N GLN D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 873 " --> pdb=" O MET D 869 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 883 " --> pdb=" O ALA D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.079A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.840A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.605A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.573A pdb=" N ASN D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.675A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.987A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.039A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.627A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.457A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.202A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.015A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.403A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.359A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'B' and resid 721 through 722 Processing sheet with id=AB6, first strand: chain 'B' and resid 721 through 722 removed outlier: 3.784A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.793A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.688A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.501A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.681A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.231A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.543A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.549A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.365A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'C' and resid 717 through 722 removed outlier: 6.922A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.596A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.013A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.252A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.966A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.601A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.838A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.847A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.043A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.283A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 673 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.690A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.803A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'D' and resid 1120 through 1122 1146 hydrogen bonds defined for protein. 3177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9636 1.35 - 1.47: 7670 1.47 - 1.60: 12944 1.60 - 1.72: 0 1.72 - 1.84: 194 Bond restraints: 30444 Sorted by residual: bond pdb=" C PHE B 497 " pdb=" N GLN B 498 " ideal model delta sigma weight residual 1.327 1.358 -0.031 1.71e-02 3.42e+03 3.30e+00 bond pdb=" N SER A 19 " pdb=" CA SER A 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN C 14 " pdb=" CA GLN C 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+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 2.78e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 30439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 40024 1.30 - 2.60: 1109 2.60 - 3.90: 130 3.90 - 5.19: 121 5.19 - 6.49: 12 Bond angle restraints: 41396 Sorted by residual: angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 106.21 109.52 -3.31 1.07e+00 8.73e-01 9.57e+00 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.12 109.54 2.58 8.40e-01 1.42e+00 9.42e+00 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 126.27 -3.81 1.41e+00 5.03e-01 7.29e+00 angle pdb=" C LEU B 916 " pdb=" CA LEU B 916 " pdb=" CB LEU B 916 " ideal model delta sigma weight residual 110.96 107.45 3.51 1.54e+00 4.22e-01 5.20e+00 angle pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta sigma weight residual 127.00 132.42 -5.42 2.40e+00 1.74e-01 5.11e+00 ... (remaining 41391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16876 17.80 - 35.59: 1022 35.59 - 53.39: 163 53.39 - 71.18: 54 71.18 - 88.98: 21 Dihedral angle restraints: 18136 sinusoidal: 7139 harmonic: 10997 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -125.67 39.67 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -47.04 -38.96 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 127.72 -34.72 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3303 0.037 - 0.074: 899 0.074 - 0.112: 290 0.112 - 0.149: 120 0.149 - 0.186: 4 Chirality restraints: 4616 Sorted by residual: chirality pdb=" CA ILE D 896 " pdb=" N ILE D 896 " pdb=" C ILE D 896 " pdb=" CB ILE D 896 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA ILE C 896 " pdb=" N ILE C 896 " pdb=" C ILE C 896 " pdb=" CB ILE C 896 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 4613 not shown) Planarity restraints: 5375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D1068 " -0.023 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D1069 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D1069 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D1069 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO D 897 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 521 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.018 5.00e-02 4.00e+02 ... (remaining 5372 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 292 2.63 - 3.19: 25876 3.19 - 3.76: 43714 3.76 - 4.33: 63049 4.33 - 4.90: 103930 Nonbonded interactions: 236861 Sorted by model distance: nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.057 3.040 nonbonded pdb=" OG1 THR B 883 " pdb=" OH TYR C 707 " model vdw 2.058 3.040 nonbonded pdb=" O GLN C 755 " pdb=" OG SER D 968 " model vdw 2.064 3.040 nonbonded pdb=" O GLN B 755 " pdb=" OG SER C 968 " model vdw 2.077 3.040 nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 2.131 3.040 ... (remaining 236856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.220 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30486 Z= 0.172 Angle : 0.583 6.493 41480 Z= 0.325 Chirality : 0.042 0.186 4616 Planarity : 0.003 0.034 5375 Dihedral : 12.343 88.980 10934 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.03 % Allowed : 1.27 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.11), residues: 3733 helix: -2.50 (0.11), residues: 1023 sheet: -2.08 (0.17), residues: 643 loop : -2.18 (0.11), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.014 0.001 TYR D 707 PHE 0.011 0.001 PHE C1075 TRP 0.006 0.001 TRP A 203 HIS 0.004 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00374 (30444) covalent geometry : angle 0.58164 (41396) SS BOND : bond 0.00430 ( 42) SS BOND : angle 0.94884 ( 84) hydrogen bonds : bond 0.27310 ( 1142) hydrogen bonds : angle 9.13929 ( 3177) *********************** 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 763 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 762 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.7579 (m-90) cc_final: 0.7315 (m-90) REVERT: B 140 PHE cc_start: 0.6176 (p90) cc_final: 0.5899 (p90) REVERT: B 191 GLU cc_start: 0.8119 (tt0) cc_final: 0.7717 (tp30) REVERT: B 202 LYS cc_start: 0.7441 (mttt) cc_final: 0.7082 (mtpp) REVERT: B 398 ASP cc_start: 0.3477 (m-30) cc_final: 0.3217 (m-30) REVERT: B 534 VAL cc_start: 0.8161 (t) cc_final: 0.7825 (m) REVERT: B 541 PHE cc_start: 0.6590 (m-80) cc_final: 0.6327 (m-80) REVERT: B 546 LEU cc_start: 0.5887 (mm) cc_final: 0.5665 (tp) REVERT: B 559 PHE cc_start: 0.6082 (p90) cc_final: 0.5538 (p90) REVERT: B 568 ASP cc_start: 0.7517 (p0) cc_final: 0.6926 (p0) REVERT: B 574 ASP cc_start: 0.8324 (t70) cc_final: 0.8004 (m-30) REVERT: C 36 VAL cc_start: 0.8669 (t) cc_final: 0.8307 (m) REVERT: C 129 LYS cc_start: 0.7686 (mttt) cc_final: 0.7355 (mtpp) REVERT: C 238 PHE cc_start: 0.7867 (p90) cc_final: 0.7410 (p90) REVERT: C 584 ILE cc_start: 0.8435 (mt) cc_final: 0.8230 (mt) REVERT: A 35 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7639 (mt-10) REVERT: A 64 ASN cc_start: 0.7388 (m-40) cc_final: 0.6981 (t0) REVERT: A 82 MET cc_start: 0.6887 (mmm) cc_final: 0.6656 (mmt) REVERT: A 322 ASN cc_start: 0.5444 (p0) cc_final: 0.4737 (t0) REVERT: A 482 ARG cc_start: 0.7411 (mtm180) cc_final: 0.7103 (mtp85) REVERT: A 557 MET cc_start: 0.5582 (ttp) cc_final: 0.5150 (mpp) REVERT: D 81 ASN cc_start: 0.5601 (t0) cc_final: 0.4834 (t0) REVERT: D 195 LYS cc_start: 0.8996 (tttt) cc_final: 0.8469 (ttpt) REVERT: D 224 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7975 (mp0) REVERT: D 239 GLN cc_start: 0.7713 (tt0) cc_final: 0.7228 (tt0) REVERT: D 284 THR cc_start: 0.7640 (m) cc_final: 0.7266 (p) REVERT: D 365 TYR cc_start: 0.7664 (m-80) cc_final: 0.7289 (m-80) REVERT: D 368 LEU cc_start: 0.7968 (tp) cc_final: 0.7696 (tp) REVERT: D 387 LEU cc_start: 0.6770 (mt) cc_final: 0.6286 (mt) REVERT: D 398 ASP cc_start: 0.7670 (m-30) cc_final: 0.7276 (m-30) REVERT: D 405 ASP cc_start: 0.8041 (m-30) cc_final: 0.7260 (p0) REVERT: D 421 TYR cc_start: 0.6769 (m-80) cc_final: 0.6494 (m-10) REVERT: D 441 LEU cc_start: 0.6506 (mt) cc_final: 0.6022 (mp) REVERT: D 542 ASN cc_start: 0.8504 (t0) cc_final: 0.8071 (t0) REVERT: D 586 ASP cc_start: 0.7219 (t70) cc_final: 0.6908 (t0) REVERT: D 856 ASN cc_start: 0.7314 (m-40) cc_final: 0.7055 (m-40) REVERT: D 979 ASP cc_start: 0.8417 (m-30) cc_final: 0.8179 (m-30) REVERT: D 1114 ILE cc_start: 0.8889 (mm) cc_final: 0.8619 (mm) outliers start: 1 outliers final: 1 residues processed: 763 average time/residue: 0.1965 time to fit residues: 234.8009 Evaluate side-chains 370 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 185 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 360 ASN B 394 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 66 HIS C 99 ASN C 334 ASN C 544 ASN C 703 ASN C 751 ASN C 787 GLN C 914 ASN C 965 GLN A 34 HIS A 81 GLN A 121 ASN A 290 ASN A 429 GLN D 99 ASN D 125 ASN D 239 GLN D 641 ASN D 787 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.155016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.125338 restraints weight = 86231.758| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.84 r_work: 0.3795 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 30486 Z= 0.310 Angle : 0.779 12.036 41480 Z= 0.411 Chirality : 0.051 0.248 4616 Planarity : 0.006 0.062 5375 Dihedral : 5.177 43.585 4051 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 10.99 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.12), residues: 3733 helix: -0.60 (0.15), residues: 1022 sheet: -1.31 (0.17), residues: 711 loop : -1.56 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.023 0.003 TYR A 381 PHE 0.033 0.003 PHE C 643 TRP 0.024 0.002 TRP A 48 HIS 0.012 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00713 (30444) covalent geometry : angle 0.77432 (41396) SS BOND : bond 0.00572 ( 42) SS BOND : angle 1.96740 ( 84) hydrogen bonds : bond 0.05323 ( 1142) hydrogen bonds : angle 6.06771 ( 3177) *********************** 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 517 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 431 time to evaluate : 0.999 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 88 ASP cc_start: 0.5970 (p0) cc_final: 0.5434 (t70) REVERT: B 104 TRP cc_start: 0.7994 (m-90) cc_final: 0.7527 (m-90) REVERT: B 106 PHE cc_start: 0.6931 (m-80) cc_final: 0.5919 (m-80) REVERT: B 168 PHE cc_start: 0.6505 (t80) cc_final: 0.6219 (t80) REVERT: B 241 LEU cc_start: 0.7280 (mt) cc_final: 0.6965 (mp) REVERT: B 456 PHE cc_start: 0.6346 (m-80) cc_final: 0.5948 (m-80) REVERT: B 787 GLN cc_start: 0.8167 (pt0) cc_final: 0.7840 (pt0) REVERT: B 904 TYR cc_start: 0.8524 (m-80) cc_final: 0.8250 (m-10) REVERT: C 191 GLU cc_start: 0.6420 (tt0) cc_final: 0.5435 (tt0) REVERT: C 584 ILE cc_start: 0.7736 (mt) cc_final: 0.7503 (mt) REVERT: C 603 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.7994 (t0) REVERT: C 796 ASP cc_start: 0.7554 (t0) cc_final: 0.7327 (p0) REVERT: C 904 TYR cc_start: 0.7591 (t80) cc_final: 0.6902 (t80) REVERT: C 1019 ARG cc_start: 0.8233 (tpt170) cc_final: 0.7978 (tpt170) REVERT: A 35 GLU cc_start: 0.7917 (mt-10) cc_final: 0.6580 (tp30) REVERT: A 323 MET cc_start: 0.2710 (mmt) cc_final: 0.2069 (mtt) REVERT: A 376 MET cc_start: 0.3316 (mtt) cc_final: 0.2229 (mmp) REVERT: A 482 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7010 (mtp85) REVERT: A 601 ASN cc_start: 0.5076 (t0) cc_final: 0.4825 (t0) REVERT: D 338 PHE cc_start: 0.6006 (p90) cc_final: 0.5692 (p90) REVERT: D 516 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6590 (mp0) REVERT: D 544 ASN cc_start: 0.7710 (p0) cc_final: 0.7308 (t0) REVERT: D 574 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7997 (t0) REVERT: D 586 ASP cc_start: 0.7281 (t70) cc_final: 0.7015 (t0) REVERT: D 856 ASN cc_start: 0.7552 (m-40) cc_final: 0.7332 (m-40) REVERT: D 985 ASP cc_start: 0.8124 (p0) cc_final: 0.7776 (m-30) outliers start: 86 outliers final: 42 residues processed: 495 average time/residue: 0.1709 time to fit residues: 139.2250 Evaluate side-chains 347 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 968 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 203 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 253 optimal weight: 0.2980 chunk 288 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 960 ASN B1106 GLN C 99 ASN C 787 GLN C 907 ASN C 969 ASN A 34 HIS ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS D 703 ASN D 762 GLN D 774 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 ASN D1106 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.158753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.129445 restraints weight = 85279.274| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.90 r_work: 0.3850 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 30486 Z= 0.117 Angle : 0.552 12.400 41480 Z= 0.285 Chirality : 0.044 0.218 4616 Planarity : 0.004 0.076 5375 Dihedral : 4.247 23.790 4050 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.06 % Allowed : 13.81 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 3733 helix: 0.43 (0.16), residues: 1043 sheet: -0.89 (0.18), residues: 744 loop : -1.22 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 102 TYR 0.018 0.001 TYR A 381 PHE 0.025 0.001 PHE B 377 TRP 0.011 0.001 TRP A 473 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00265 (30444) covalent geometry : angle 0.54513 (41396) SS BOND : bond 0.00693 ( 42) SS BOND : angle 1.98719 ( 84) hydrogen bonds : bond 0.03940 ( 1142) hydrogen bonds : angle 5.40435 ( 3177) *********************** 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 478 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 410 time to evaluate : 1.058 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 88 ASP cc_start: 0.5927 (p0) cc_final: 0.5617 (t0) REVERT: B 317 ASN cc_start: 0.8072 (m-40) cc_final: 0.7221 (m-40) REVERT: B 319 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7766 (tpp80) REVERT: B 456 PHE cc_start: 0.6646 (m-80) cc_final: 0.6431 (m-80) REVERT: B 585 LEU cc_start: 0.5065 (pp) cc_final: 0.4845 (tt) REVERT: B 787 GLN cc_start: 0.8258 (pt0) cc_final: 0.7861 (pt0) REVERT: B 994 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8173 (t0) REVERT: C 92 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 191 GLU cc_start: 0.6385 (tt0) cc_final: 0.5874 (mt-10) REVERT: C 708 SER cc_start: 0.8561 (p) cc_final: 0.8074 (m) REVERT: C 796 ASP cc_start: 0.7685 (t0) cc_final: 0.7473 (p0) REVERT: C 825 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8542 (mtpp) REVERT: C 884 SER cc_start: 0.9455 (m) cc_final: 0.9223 (p) REVERT: C 904 TYR cc_start: 0.7717 (t80) cc_final: 0.7059 (t80) REVERT: A 35 GLU cc_start: 0.7950 (mt-10) cc_final: 0.6631 (tp30) REVERT: A 82 MET cc_start: 0.5387 (mtt) cc_final: 0.4921 (mtm) REVERT: A 376 MET cc_start: 0.3377 (mtt) cc_final: 0.2705 (mmp) REVERT: A 482 ARG cc_start: 0.7797 (mtm180) cc_final: 0.7374 (mtp180) REVERT: D 273 ARG cc_start: 0.8438 (mmt90) cc_final: 0.8095 (mmm160) REVERT: D 398 ASP cc_start: 0.7375 (m-30) cc_final: 0.6550 (m-30) REVERT: D 489 TYR cc_start: 0.5995 (t80) cc_final: 0.4439 (m-10) REVERT: D 516 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6355 (mp0) REVERT: D 524 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.7062 (t) REVERT: D 703 ASN cc_start: 0.8782 (t0) cc_final: 0.8528 (t0) REVERT: D 740 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8582 (tpp) REVERT: D 751 ASN cc_start: 0.8865 (m-40) cc_final: 0.8564 (m110) REVERT: D 856 ASN cc_start: 0.7623 (m-40) cc_final: 0.7371 (m-40) REVERT: D 979 ASP cc_start: 0.8802 (m-30) cc_final: 0.7979 (t0) REVERT: D 985 ASP cc_start: 0.8201 (p0) cc_final: 0.7918 (p0) REVERT: D 995 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7936 (tpp80) REVERT: D 1114 ILE cc_start: 0.9145 (mm) cc_final: 0.8753 (mm) outliers start: 68 outliers final: 39 residues processed: 453 average time/residue: 0.1730 time to fit residues: 130.2547 Evaluate side-chains 376 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 130 optimal weight: 0.9990 chunk 303 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 372 optimal weight: 0.8980 chunk 89 optimal weight: 0.0270 chunk 198 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 362 optimal weight: 5.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 317 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 787 GLN A 401 HIS D 703 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.158436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.129399 restraints weight = 84965.444| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.06 r_work: 0.3835 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4835 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= 0.115 Angle : 0.533 13.664 41480 Z= 0.273 Chirality : 0.043 0.237 4616 Planarity : 0.004 0.064 5375 Dihedral : 4.063 19.399 4050 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 14.51 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3733 helix: 0.80 (0.16), residues: 1029 sheet: -0.62 (0.18), residues: 773 loop : -1.06 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.017 0.001 TYR B 453 PHE 0.024 0.001 PHE B 377 TRP 0.027 0.001 TRP D 258 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00256 (30444) covalent geometry : angle 0.52739 (41396) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.84714 ( 84) hydrogen bonds : bond 0.03626 ( 1142) hydrogen bonds : angle 5.14916 ( 3177) *********************** 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 461 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 378 time to evaluate : 1.202 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 191 GLU cc_start: 0.6017 (tp30) cc_final: 0.5675 (tt0) REVERT: B 456 PHE cc_start: 0.6419 (m-80) cc_final: 0.6155 (m-80) REVERT: B 779 GLN cc_start: 0.8678 (tp40) cc_final: 0.8435 (tt0) REVERT: B 787 GLN cc_start: 0.7916 (pt0) cc_final: 0.7479 (pt0) REVERT: C 92 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7495 (t80) REVERT: C 191 GLU cc_start: 0.6300 (tt0) cc_final: 0.5851 (mt-10) REVERT: C 241 LEU cc_start: 0.8084 (mp) cc_final: 0.7862 (mt) REVERT: C 336 CYS cc_start: 0.2099 (OUTLIER) cc_final: 0.0949 (t) REVERT: C 409 GLN cc_start: 0.0995 (mt0) cc_final: 0.0620 (pt0) REVERT: C 708 SER cc_start: 0.8347 (p) cc_final: 0.7866 (m) REVERT: C 904 TYR cc_start: 0.7393 (t80) cc_final: 0.6936 (t80) REVERT: A 35 GLU cc_start: 0.7938 (mt-10) cc_final: 0.6635 (tp30) REVERT: A 82 MET cc_start: 0.5746 (mtt) cc_final: 0.5235 (mtm) REVERT: A 297 MET cc_start: 0.1931 (ptp) cc_final: 0.1687 (ptp) REVERT: A 322 ASN cc_start: 0.5273 (p0) cc_final: 0.4749 (t0) REVERT: A 366 MET cc_start: 0.2664 (tpt) cc_final: 0.2432 (mmm) REVERT: A 376 MET cc_start: 0.3500 (mtt) cc_final: 0.3212 (mmm) REVERT: A 482 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7332 (mtp180) REVERT: D 273 ARG cc_start: 0.8330 (mmt90) cc_final: 0.8047 (mmm160) REVERT: D 516 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6415 (mp0) REVERT: D 524 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7301 (t) REVERT: D 703 ASN cc_start: 0.8716 (t0) cc_final: 0.8318 (t0) REVERT: D 751 ASN cc_start: 0.8724 (m-40) cc_final: 0.8492 (m110) REVERT: D 856 ASN cc_start: 0.7437 (m-40) cc_final: 0.7219 (m-40) REVERT: D 979 ASP cc_start: 0.8554 (m-30) cc_final: 0.7921 (t0) REVERT: D 1114 ILE cc_start: 0.9125 (mm) cc_final: 0.8727 (mm) outliers start: 83 outliers final: 55 residues processed: 432 average time/residue: 0.1806 time to fit residues: 128.6118 Evaluate side-chains 385 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 327 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 945 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 118 optimal weight: 0.7980 chunk 347 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 655 HIS C 703 ASN D 115 GLN D 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.156341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.127278 restraints weight = 85224.223| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.84 r_work: 0.3811 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30486 Z= 0.143 Angle : 0.554 13.037 41480 Z= 0.285 Chirality : 0.044 0.225 4616 Planarity : 0.004 0.059 5375 Dihedral : 4.258 29.853 4050 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.79 % Allowed : 15.45 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3733 helix: 0.83 (0.16), residues: 1048 sheet: -0.50 (0.18), residues: 736 loop : -0.95 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 815 TYR 0.017 0.001 TYR A 41 PHE 0.022 0.002 PHE B 168 TRP 0.021 0.001 TRP D 258 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00330 (30444) covalent geometry : angle 0.54778 (41396) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.89844 ( 84) hydrogen bonds : bond 0.03707 ( 1142) hydrogen bonds : angle 5.15681 ( 3177) *********************** 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 438 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 346 time to evaluate : 1.119 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 191 GLU cc_start: 0.5620 (tp30) cc_final: 0.4790 (tt0) REVERT: B 456 PHE cc_start: 0.6536 (m-80) cc_final: 0.6199 (m-80) REVERT: B 779 GLN cc_start: 0.8616 (tp40) cc_final: 0.8373 (tt0) REVERT: B 787 GLN cc_start: 0.7905 (pt0) cc_final: 0.7493 (pt0) REVERT: C 92 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7485 (t80) REVERT: C 324 GLU cc_start: 0.7456 (mp0) cc_final: 0.7229 (pm20) REVERT: C 336 CYS cc_start: 0.2075 (OUTLIER) cc_final: 0.0914 (t) REVERT: C 342 PHE cc_start: 0.5525 (m-80) cc_final: 0.5318 (m-80) REVERT: C 708 SER cc_start: 0.8461 (p) cc_final: 0.7941 (m) REVERT: C 796 ASP cc_start: 0.7554 (p0) cc_final: 0.7282 (p0) REVERT: C 904 TYR cc_start: 0.7450 (t80) cc_final: 0.6846 (t80) REVERT: A 35 GLU cc_start: 0.7887 (mt-10) cc_final: 0.6579 (tp30) REVERT: A 82 MET cc_start: 0.6002 (mtt) cc_final: 0.5584 (mtm) REVERT: A 376 MET cc_start: 0.3449 (mtt) cc_final: 0.3227 (mmt) REVERT: A 482 ARG cc_start: 0.7787 (mtm180) cc_final: 0.7317 (mtp85) REVERT: D 129 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7400 (tppt) REVERT: D 233 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 495 TYR cc_start: 0.4602 (m-80) cc_final: 0.4253 (m-80) REVERT: D 516 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6476 (mp0) REVERT: D 703 ASN cc_start: 0.8781 (t0) cc_final: 0.8427 (t0) REVERT: D 751 ASN cc_start: 0.8773 (m-40) cc_final: 0.8539 (m110) REVERT: D 856 ASN cc_start: 0.7573 (m-40) cc_final: 0.7371 (m-40) REVERT: D 896 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7856 (mt) REVERT: D 979 ASP cc_start: 0.8461 (m-30) cc_final: 0.7970 (t0) outliers start: 92 outliers final: 67 residues processed: 406 average time/residue: 0.1734 time to fit residues: 117.7402 Evaluate side-chains 387 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 316 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 945 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 175 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 345 optimal weight: 0.0980 chunk 105 optimal weight: 0.1980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1142 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.155938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.126857 restraints weight = 84610.177| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.00 r_work: 0.3808 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30486 Z= 0.135 Angle : 0.541 13.034 41480 Z= 0.279 Chirality : 0.043 0.162 4616 Planarity : 0.004 0.057 5375 Dihedral : 4.229 24.283 4050 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.09 % Allowed : 15.87 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3733 helix: 0.95 (0.17), residues: 1028 sheet: -0.42 (0.19), residues: 736 loop : -0.93 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 815 TYR 0.060 0.001 TYR A 41 PHE 0.022 0.001 PHE B 377 TRP 0.026 0.001 TRP A 610 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00310 (30444) covalent geometry : angle 0.53581 (41396) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.76412 ( 84) hydrogen bonds : bond 0.03582 ( 1142) hydrogen bonds : angle 5.08300 ( 3177) *********************** 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 440 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 338 time to evaluate : 1.094 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 153 MET cc_start: 0.0748 (OUTLIER) cc_final: 0.0042 (tmm) REVERT: B 168 PHE cc_start: 0.6349 (t80) cc_final: 0.6073 (t80) REVERT: B 191 GLU cc_start: 0.5760 (tp30) cc_final: 0.5400 (tp30) REVERT: B 456 PHE cc_start: 0.6676 (m-80) cc_final: 0.6313 (m-80) REVERT: B 585 LEU cc_start: 0.6200 (tp) cc_final: 0.5893 (mt) REVERT: B 779 GLN cc_start: 0.8600 (tp40) cc_final: 0.8380 (tt0) REVERT: B 787 GLN cc_start: 0.7965 (pt0) cc_final: 0.7605 (pt0) REVERT: C 92 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7549 (t80) REVERT: C 324 GLU cc_start: 0.7567 (mp0) cc_final: 0.7196 (pm20) REVERT: C 336 CYS cc_start: 0.2192 (OUTLIER) cc_final: 0.1040 (t) REVERT: C 703 ASN cc_start: 0.8803 (t0) cc_final: 0.7793 (t0) REVERT: C 740 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8267 (ttp) REVERT: C 904 TYR cc_start: 0.7499 (t80) cc_final: 0.6984 (t80) REVERT: A 35 GLU cc_start: 0.7852 (mt-10) cc_final: 0.6531 (tp30) REVERT: A 82 MET cc_start: 0.6391 (mtt) cc_final: 0.5950 (mtm) REVERT: A 297 MET cc_start: 0.1401 (ptp) cc_final: -0.0392 (ptp) REVERT: A 325 GLN cc_start: 0.7094 (tp40) cc_final: 0.5661 (pt0) REVERT: A 482 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7362 (mtp85) REVERT: D 495 TYR cc_start: 0.4704 (m-80) cc_final: 0.4429 (m-80) REVERT: D 516 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6605 (mp0) REVERT: D 703 ASN cc_start: 0.8763 (t0) cc_final: 0.8549 (t0) REVERT: D 751 ASN cc_start: 0.8793 (m-40) cc_final: 0.8577 (m110) REVERT: D 856 ASN cc_start: 0.7414 (m-40) cc_final: 0.7117 (m-40) REVERT: D 896 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7591 (mt) REVERT: D 979 ASP cc_start: 0.8465 (m-30) cc_final: 0.7886 (t0) outliers start: 102 outliers final: 72 residues processed: 409 average time/residue: 0.1754 time to fit residues: 119.7109 Evaluate side-chains 389 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 312 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 486 PHE Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 945 LEU Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 135 optimal weight: 0.9990 chunk 346 optimal weight: 0.0370 chunk 214 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 301 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 505 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.157081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.128922 restraints weight = 84988.737| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.04 r_work: 0.3827 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30486 Z= 0.114 Angle : 0.532 12.723 41480 Z= 0.271 Chirality : 0.043 0.188 4616 Planarity : 0.004 0.068 5375 Dihedral : 4.198 32.353 4050 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.63 % Allowed : 17.11 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.14), residues: 3733 helix: 1.04 (0.17), residues: 1030 sheet: -0.31 (0.19), residues: 726 loop : -0.88 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 815 TYR 0.036 0.001 TYR A 41 PHE 0.022 0.001 PHE B 377 TRP 0.017 0.001 TRP A 610 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00260 (30444) covalent geometry : angle 0.52756 (41396) SS BOND : bond 0.00515 ( 42) SS BOND : angle 1.65980 ( 84) hydrogen bonds : bond 0.03418 ( 1142) hydrogen bonds : angle 5.01756 ( 3177) *********************** 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 427 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 340 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.6470 (t80) cc_final: 0.5943 (t80) REVERT: B 153 MET cc_start: 0.0701 (OUTLIER) cc_final: 0.0125 (tmm) REVERT: B 191 GLU cc_start: 0.5808 (tp30) cc_final: 0.5455 (tp30) REVERT: B 456 PHE cc_start: 0.6701 (m-80) cc_final: 0.6395 (m-80) REVERT: B 585 LEU cc_start: 0.6205 (tp) cc_final: 0.5830 (mt) REVERT: B 779 GLN cc_start: 0.8638 (tp40) cc_final: 0.8403 (tt0) REVERT: B 787 GLN cc_start: 0.7947 (pt0) cc_final: 0.7554 (pt0) REVERT: B 965 GLN cc_start: 0.8211 (tt0) cc_final: 0.7974 (tt0) REVERT: C 92 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7577 (t80) REVERT: C 336 CYS cc_start: 0.2159 (OUTLIER) cc_final: 0.1019 (t) REVERT: C 409 GLN cc_start: 0.0665 (mt0) cc_final: 0.0101 (pt0) REVERT: C 703 ASN cc_start: 0.8719 (t0) cc_final: 0.7666 (t0) REVERT: C 740 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8289 (ttp) REVERT: C 796 ASP cc_start: 0.7477 (p0) cc_final: 0.7154 (p0) REVERT: C 904 TYR cc_start: 0.7518 (t80) cc_final: 0.6942 (t80) REVERT: A 35 GLU cc_start: 0.7852 (mt-10) cc_final: 0.6430 (tm-30) REVERT: A 325 GLN cc_start: 0.6997 (tp40) cc_final: 0.5581 (pt0) REVERT: A 482 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7419 (mtp85) REVERT: D 291 CYS cc_start: 0.7286 (m) cc_final: 0.7016 (m) REVERT: D 495 TYR cc_start: 0.4820 (m-80) cc_final: 0.4243 (m-80) REVERT: D 516 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6620 (mp0) REVERT: D 751 ASN cc_start: 0.8775 (m-40) cc_final: 0.8568 (m110) REVERT: D 896 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7538 (mt) REVERT: D 979 ASP cc_start: 0.8368 (m-30) cc_final: 0.7978 (t0) REVERT: D 1072 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7505 (mt-10) outliers start: 87 outliers final: 67 residues processed: 399 average time/residue: 0.1705 time to fit residues: 113.6394 Evaluate side-chains 383 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 310 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 486 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 66 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 242 optimal weight: 0.8980 chunk 374 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 246 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN C1071 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.158535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.130740 restraints weight = 85858.679| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.90 r_work: 0.3834 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 30486 Z= 0.108 Angle : 0.528 12.663 41480 Z= 0.270 Chirality : 0.043 0.177 4616 Planarity : 0.004 0.060 5375 Dihedral : 4.094 28.351 4050 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.51 % Allowed : 17.32 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3733 helix: 1.18 (0.17), residues: 1019 sheet: -0.31 (0.19), residues: 740 loop : -0.85 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.029 0.001 TYR A 41 PHE 0.036 0.001 PHE D 541 TRP 0.012 0.001 TRP A 610 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00245 (30444) covalent geometry : angle 0.52340 (41396) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.67342 ( 84) hydrogen bonds : bond 0.03335 ( 1142) hydrogen bonds : angle 4.92772 ( 3177) *********************** 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 413 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 330 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.0890 (OUTLIER) cc_final: 0.0292 (tmm) REVERT: B 191 GLU cc_start: 0.5765 (tp30) cc_final: 0.5402 (tp30) REVERT: B 456 PHE cc_start: 0.6569 (m-80) cc_final: 0.6291 (m-80) REVERT: B 585 LEU cc_start: 0.6112 (tp) cc_final: 0.5767 (mt) REVERT: B 787 GLN cc_start: 0.7908 (pt0) cc_final: 0.7556 (pt0) REVERT: C 191 GLU cc_start: 0.7077 (tt0) cc_final: 0.6794 (tp30) REVERT: C 336 CYS cc_start: 0.2094 (OUTLIER) cc_final: 0.0961 (t) REVERT: C 703 ASN cc_start: 0.8741 (t0) cc_final: 0.7722 (t0) REVERT: C 740 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8246 (ttp) REVERT: C 904 TYR cc_start: 0.7460 (t80) cc_final: 0.6929 (t80) REVERT: C 1029 MET cc_start: 0.8699 (tpp) cc_final: 0.8339 (ttm) REVERT: A 35 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6396 (tm-30) REVERT: A 325 GLN cc_start: 0.6978 (tp40) cc_final: 0.5582 (pt0) REVERT: D 291 CYS cc_start: 0.7304 (m) cc_final: 0.7019 (m) REVERT: D 495 TYR cc_start: 0.4879 (m-80) cc_final: 0.4342 (m-80) REVERT: D 516 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6597 (mp0) REVERT: D 896 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7262 (mt) REVERT: D 979 ASP cc_start: 0.8326 (m-30) cc_final: 0.7978 (t0) REVERT: D 1072 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7413 (mt-10) outliers start: 83 outliers final: 68 residues processed: 390 average time/residue: 0.1664 time to fit residues: 109.3694 Evaluate side-chains 383 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 310 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 200 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 955 ASN C 751 ASN C 779 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.154695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124202 restraints weight = 84922.326| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.14 r_work: 0.3776 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30486 Z= 0.172 Angle : 0.599 12.794 41480 Z= 0.308 Chirality : 0.045 0.215 4616 Planarity : 0.004 0.057 5375 Dihedral : 4.519 28.061 4050 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.79 % Allowed : 17.38 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3733 helix: 0.95 (0.17), residues: 1012 sheet: -0.34 (0.19), residues: 724 loop : -0.94 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 190 TYR 0.022 0.002 TYR A 41 PHE 0.030 0.002 PHE B 168 TRP 0.016 0.002 TRP D 258 HIS 0.006 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00397 (30444) covalent geometry : angle 0.59416 (41396) SS BOND : bond 0.00460 ( 42) SS BOND : angle 1.80366 ( 84) hydrogen bonds : bond 0.03974 ( 1142) hydrogen bonds : angle 5.20692 ( 3177) *********************** 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 401 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 309 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 PHE cc_start: 0.5628 (p90) cc_final: 0.5337 (p90) REVERT: B 153 MET cc_start: 0.0201 (OUTLIER) cc_final: -0.0593 (tmm) REVERT: B 456 PHE cc_start: 0.6709 (m-80) cc_final: 0.6354 (m-80) REVERT: B 1107 ARG cc_start: 0.7805 (mtt180) cc_final: 0.6741 (tpt170) REVERT: C 191 GLU cc_start: 0.7302 (tt0) cc_final: 0.6853 (tp30) REVERT: C 740 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8300 (ttp) REVERT: C 904 TYR cc_start: 0.7646 (t80) cc_final: 0.7173 (t80) REVERT: C 1029 MET cc_start: 0.8747 (tpp) cc_final: 0.8450 (ttm) REVERT: C 1041 ASP cc_start: 0.7917 (m-30) cc_final: 0.7593 (m-30) REVERT: A 35 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6314 (tm-30) REVERT: A 45 LEU cc_start: 0.6835 (pp) cc_final: 0.6546 (mt) REVERT: A 325 GLN cc_start: 0.7210 (tp40) cc_final: 0.5837 (pt0) REVERT: A 482 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7570 (mmm160) REVERT: D 129 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7900 (mmtp) REVERT: D 291 CYS cc_start: 0.7384 (m) cc_final: 0.7129 (m) REVERT: D 495 TYR cc_start: 0.4781 (m-80) cc_final: 0.4494 (m-80) REVERT: D 516 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6714 (mp0) REVERT: D 979 ASP cc_start: 0.8430 (m-30) cc_final: 0.8038 (t0) REVERT: D 985 ASP cc_start: 0.7611 (p0) cc_final: 0.7274 (p0) REVERT: D 1072 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7562 (mt-10) outliers start: 92 outliers final: 77 residues processed: 379 average time/residue: 0.1671 time to fit residues: 106.3678 Evaluate side-chains 374 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 294 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 194 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 310 optimal weight: 8.9990 chunk 44 optimal weight: 0.0870 chunk 22 optimal weight: 9.9990 chunk 125 optimal weight: 0.0370 chunk 279 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.158776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131324 restraints weight = 85868.178| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.02 r_work: 0.3847 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30486 Z= 0.101 Angle : 0.536 12.058 41480 Z= 0.273 Chirality : 0.043 0.213 4616 Planarity : 0.003 0.055 5375 Dihedral : 4.082 25.052 4050 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.09 % Allowed : 18.20 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3733 helix: 1.32 (0.17), residues: 999 sheet: -0.25 (0.19), residues: 726 loop : -0.84 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 815 TYR 0.025 0.001 TYR A 41 PHE 0.030 0.001 PHE B 168 TRP 0.024 0.001 TRP B 104 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00227 (30444) covalent geometry : angle 0.53278 (41396) SS BOND : bond 0.00354 ( 42) SS BOND : angle 1.47935 ( 84) hydrogen bonds : bond 0.03273 ( 1142) hydrogen bonds : angle 4.93173 ( 3177) ********************** 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 403 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5967 (m-80) REVERT: B 787 GLN cc_start: 0.8055 (pt0) cc_final: 0.7712 (pt0) REVERT: B 902 MET cc_start: 0.8626 (tpp) cc_final: 0.8395 (mmt) REVERT: C 191 GLU cc_start: 0.7352 (tt0) cc_final: 0.7053 (tp30) REVERT: C 409 GLN cc_start: 0.0722 (mt0) cc_final: 0.0415 (pt0) REVERT: C 703 ASN cc_start: 0.8864 (t0) cc_final: 0.8068 (t0) REVERT: C 740 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: C 904 TYR cc_start: 0.7688 (t80) cc_final: 0.7273 (t80) REVERT: C 917 TYR cc_start: 0.9096 (m-80) cc_final: 0.8867 (m-80) REVERT: A 35 GLU cc_start: 0.7844 (mt-10) cc_final: 0.6404 (tm-30) REVERT: A 45 LEU cc_start: 0.6913 (pp) cc_final: 0.6681 (mt) REVERT: A 325 GLN cc_start: 0.7242 (tp40) cc_final: 0.6000 (pt0) REVERT: A 482 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7570 (mmm160) REVERT: D 291 CYS cc_start: 0.7914 (m) cc_final: 0.7677 (m) REVERT: D 452 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8054 (ttp-110) REVERT: D 495 TYR cc_start: 0.5063 (m-80) cc_final: 0.4541 (m-80) REVERT: D 516 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6670 (mp0) REVERT: D 896 ILE cc_start: 0.7928 (mm) cc_final: 0.7687 (mt) REVERT: D 979 ASP cc_start: 0.8381 (m-30) cc_final: 0.8085 (t0) REVERT: D 985 ASP cc_start: 0.7777 (p0) cc_final: 0.7440 (p0) REVERT: D 1072 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7592 (mt-10) outliers start: 69 outliers final: 56 residues processed: 380 average time/residue: 0.1641 time to fit residues: 104.8707 Evaluate side-chains 370 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 311 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 312 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.154995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.124995 restraints weight = 84791.869| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.17 r_work: 0.3780 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30486 Z= 0.169 Angle : 0.596 14.682 41480 Z= 0.307 Chirality : 0.045 0.180 4616 Planarity : 0.004 0.057 5375 Dihedral : 4.471 24.447 4050 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.39 % Allowed : 18.14 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3733 helix: 1.07 (0.17), residues: 1009 sheet: -0.25 (0.19), residues: 719 loop : -0.92 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 815 TYR 0.022 0.002 TYR D 91 PHE 0.032 0.002 PHE B 168 TRP 0.021 0.002 TRP B 104 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00394 (30444) covalent geometry : angle 0.58968 (41396) SS BOND : bond 0.00525 ( 42) SS BOND : angle 1.96546 ( 84) hydrogen bonds : bond 0.03872 ( 1142) hydrogen bonds : angle 5.18492 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8471.51 seconds wall clock time: 145 minutes 26.77 seconds (8726.77 seconds total)