Starting phenix.real_space_refine on Wed Jun 25 21:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9b_32363/06_2025/7w9b_32363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9b_32363/06_2025/7w9b_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_32363/06_2025/7w9b_32363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9b_32363/06_2025/7w9b_32363.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9b_32363/06_2025/7w9b_32363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9b_32363/06_2025/7w9b_32363.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.111 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29737 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8289 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 6 Chain: "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: 17.46, per 1000 atoms: 0.59 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: 7.16 Conformation dependent library (CDL) restraints added in 3.8 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: 4.12 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: 15.96 Time building geometry restraints manager: 8.60 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.310 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 72.370 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (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 TRP 0.006 0.001 TRP A 203 HIS 0.004 0.001 HIS A 540 PHE 0.011 0.001 PHE C1075 TYR 0.014 0.001 TYR D 707 ARG 0.003 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.27310 ( 1142) hydrogen bonds : angle 9.13929 ( 3177) SS BOND : bond 0.00430 ( 42) SS BOND : angle 0.94884 ( 84) covalent geometry : bond 0.00374 (30444) covalent geometry : angle 0.58164 (41396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 762 time to evaluate : 3.297 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: B 104 TRP cc_start: 0.7580 (m-90) cc_final: 0.7314 (m-90) REVERT: B 118 LEU cc_start: 0.8635 (tp) cc_final: 0.8372 (tp) REVERT: B 133 PHE cc_start: 0.7302 (m-80) cc_final: 0.6507 (m-80) REVERT: B 140 PHE cc_start: 0.6176 (p90) cc_final: 0.5897 (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 317 ASN cc_start: 0.7107 (m-40) cc_final: 0.6738 (m110) REVERT: B 398 ASP cc_start: 0.3477 (m-30) cc_final: 0.2261 (m-30) REVERT: B 541 PHE cc_start: 0.6590 (m-80) cc_final: 0.6298 (m-80) REVERT: B 546 LEU cc_start: 0.5887 (mm) cc_final: 0.5666 (tp) REVERT: B 559 PHE cc_start: 0.6082 (p90) cc_final: 0.5537 (p90) REVERT: B 568 ASP cc_start: 0.7517 (p0) cc_final: 0.6925 (p0) REVERT: B 574 ASP cc_start: 0.8324 (t70) cc_final: 0.8005 (m-30) REVERT: C 36 VAL cc_start: 0.8669 (t) cc_final: 0.8305 (m) REVERT: C 129 LYS cc_start: 0.7686 (mttt) cc_final: 0.7354 (mtpp) REVERT: C 238 PHE cc_start: 0.7867 (p90) cc_final: 0.7411 (p90) REVERT: C 584 ILE cc_start: 0.8435 (mt) cc_final: 0.8231 (mt) REVERT: A 35 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 64 ASN cc_start: 0.7388 (m-40) cc_final: 0.6982 (t0) REVERT: A 82 MET cc_start: 0.6887 (mmm) cc_final: 0.6660 (mmt) REVERT: A 322 ASN cc_start: 0.5444 (p0) cc_final: 0.4737 (t0) REVERT: A 457 GLU cc_start: 0.3631 (mm-30) cc_final: 0.3232 (mp0) 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: 0.8441 (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: 0.7267 (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: 0.6285 (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: 0.6450 (m-80) REVERT: D 441 LEU cc_start: 0.6506 (mt) cc_final: 0.6023 (mp) REVERT: D 542 ASN cc_start: 0.8504 (t0) cc_final: 0.8070 (t0) REVERT: D 586 ASP cc_start: 0.7219 (t70) cc_final: 0.6903 (t0) REVERT: D 856 ASN cc_start: 0.7314 (m-40) cc_final: 0.7057 (m-40) REVERT: D 979 ASP cc_start: 0.8417 (m-30) cc_final: 0.8178 (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: 0.4377 time to fit residues: 520.0472 Evaluate side-chains 374 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 3.525 ------------------------------------------------------------------------------- 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 318 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.0980 chunk 219 optimal weight: 10.0000 chunk 342 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 474 GLN B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 437 ASN C 703 ASN C 709 ASN C 751 ASN C 787 GLN C 914 ASN C 965 GLN A 81 GLN A 121 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN A 522 GLN D 66 HIS D 99 ASN D 641 ASN D 787 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.134816 restraints weight = 84783.548| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.87 r_work: 0.3922 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 30486 Z= 0.146 Angle : 0.571 8.527 41480 Z= 0.299 Chirality : 0.045 0.197 4616 Planarity : 0.004 0.042 5375 Dihedral : 4.012 48.584 4051 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.54 % Allowed : 9.18 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 3733 helix: -0.22 (0.15), residues: 1041 sheet: -1.29 (0.17), residues: 738 loop : -1.41 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 203 HIS 0.007 0.001 HIS A 195 PHE 0.020 0.002 PHE D 377 TYR 0.021 0.001 TYR A 381 ARG 0.006 0.001 ARG D 246 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 1142) hydrogen bonds : angle 5.72099 ( 3177) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.69069 ( 84) covalent geometry : bond 0.00330 (30444) covalent geometry : angle 0.56678 (41396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 480 time to evaluate : 3.194 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: B 88 ASP cc_start: 0.5743 (p0) cc_final: 0.5182 (t0) REVERT: B 104 TRP cc_start: 0.7776 (m-90) cc_final: 0.7299 (m-90) REVERT: B 106 PHE cc_start: 0.6249 (m-80) cc_final: 0.5426 (m-80) REVERT: B 133 PHE cc_start: 0.6064 (m-80) cc_final: 0.5740 (m-80) REVERT: B 270 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7619 (mt) REVERT: B 317 ASN cc_start: 0.7488 (m-40) cc_final: 0.7098 (m110) REVERT: B 393 THR cc_start: 0.7923 (p) cc_final: 0.7626 (t) REVERT: B 402 ILE cc_start: 0.5929 (pt) cc_final: 0.5346 (pt) REVERT: B 453 TYR cc_start: 0.4507 (p90) cc_final: 0.3826 (p90) REVERT: B 456 PHE cc_start: 0.6835 (m-80) cc_final: 0.6624 (m-80) REVERT: B 983 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7362 (mtm-85) REVERT: B 1142 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7982 (pp30) REVERT: C 40 ASP cc_start: 0.7127 (p0) cc_final: 0.6925 (p0) REVERT: C 129 LYS cc_start: 0.8158 (mttt) cc_final: 0.7420 (mtpp) REVERT: C 191 GLU cc_start: 0.6510 (tt0) cc_final: 0.5477 (tt0) REVERT: C 708 SER cc_start: 0.8011 (p) cc_final: 0.7569 (m) REVERT: C 914 ASN cc_start: 0.8269 (m110) cc_final: 0.8038 (m110) REVERT: C 973 ILE cc_start: 0.9290 (mm) cc_final: 0.9061 (mt) REVERT: A 35 GLU cc_start: 0.7842 (mt-10) cc_final: 0.6674 (tp30) REVERT: A 312 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.3840 (mm-30) REVERT: A 376 MET cc_start: 0.3430 (mtt) cc_final: 0.2879 (mpp) REVERT: A 482 ARG cc_start: 0.7541 (mtm180) cc_final: 0.6922 (mtp85) REVERT: A 529 LEU cc_start: 0.5310 (mm) cc_final: 0.4985 (pp) REVERT: D 223 LEU cc_start: 0.7200 (mp) cc_final: 0.6808 (mp) REVERT: D 387 LEU cc_start: 0.7069 (mt) cc_final: 0.6568 (mt) REVERT: D 516 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6444 (mp0) REVERT: D 856 ASN cc_start: 0.7537 (m-40) cc_final: 0.7306 (m-40) REVERT: D 1114 ILE cc_start: 0.9037 (mm) cc_final: 0.8770 (mm) outliers start: 51 outliers final: 28 residues processed: 515 average time/residue: 0.4701 time to fit residues: 403.3159 Evaluate side-chains 354 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 437 ASN 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 A residue 21 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 754 LEU Chi-restraints excluded: chain D residue 794 ILE 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 316 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 356 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 360 ASN B 394 ASN B 556 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 804 GLN C 99 ASN C 544 ASN C 907 ASN C 913 GLN C 969 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN A 34 HIS A 417 HIS D 370 ASN D 641 ASN D 655 HIS ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.154331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125182 restraints weight = 84877.336| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.02 r_work: 0.3783 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 30486 Z= 0.254 Angle : 0.693 13.799 41480 Z= 0.362 Chirality : 0.048 0.197 4616 Planarity : 0.005 0.059 5375 Dihedral : 4.844 39.228 4051 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.03 % Allowed : 12.36 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3733 helix: 0.23 (0.16), residues: 1030 sheet: -0.83 (0.18), residues: 761 loop : -1.32 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 48 HIS 0.007 0.001 HIS D 655 PHE 0.020 0.002 PHE D 643 TYR 0.021 0.002 TYR C 91 ARG 0.010 0.001 ARG D 815 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 1142) hydrogen bonds : angle 5.66279 ( 3177) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.29815 ( 84) covalent geometry : bond 0.00582 (30444) covalent geometry : angle 0.69160 (41396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 373 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.6076 (p0) cc_final: 0.5514 (t0) REVERT: B 110 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4091 (mp) REVERT: B 241 LEU cc_start: 0.7225 (mt) cc_final: 0.7010 (mp) REVERT: B 377 PHE cc_start: 0.3724 (p90) cc_final: 0.3481 (p90) REVERT: B 393 THR cc_start: 0.8449 (p) cc_final: 0.8242 (t) REVERT: B 456 PHE cc_start: 0.6501 (m-80) cc_final: 0.6120 (m-80) REVERT: B 787 GLN cc_start: 0.8127 (pt0) cc_final: 0.7720 (pt0) REVERT: B 1142 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8173 (pp30) REVERT: C 191 GLU cc_start: 0.6475 (tt0) cc_final: 0.5478 (tt0) REVERT: C 825 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8476 (mtpp) REVERT: C 904 TYR cc_start: 0.7604 (t80) cc_final: 0.6996 (t80) REVERT: C 1019 ARG cc_start: 0.8184 (tpt170) cc_final: 0.7955 (tpt170) REVERT: A 35 GLU cc_start: 0.7917 (mt-10) cc_final: 0.6670 (tp30) REVERT: A 376 MET cc_start: 0.3506 (mtt) cc_final: 0.2979 (mpp) REVERT: A 482 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7332 (mmt90) REVERT: D 516 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6404 (mp0) REVERT: D 751 ASN cc_start: 0.8786 (m-40) cc_final: 0.8514 (m110) REVERT: D 869 MET cc_start: 0.9002 (mtp) cc_final: 0.8787 (mtm) REVERT: D 979 ASP cc_start: 0.8673 (m-30) cc_final: 0.7920 (t0) outliers start: 100 outliers final: 66 residues processed: 452 average time/residue: 0.3894 time to fit residues: 289.0808 Evaluate side-chains 367 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 3.167 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 392 PHE 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 534 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 603 ASN 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 1104 VAL Chi-restraints excluded: chain B residue 1116 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 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 596 SER 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 709 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 368 LEU 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 560 LEU Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 641 ASN Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1051 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 373 optimal weight: 5.9990 chunk 278 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 115 GLN B 655 HIS B 703 ASN B 901 GLN C 99 ASN C 907 ASN C 969 ASN A 34 HIS A 139 GLN A 290 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 762 GLN D 914 ASN D1106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.126587 restraints weight = 85110.967| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.03 r_work: 0.3813 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30486 Z= 0.123 Angle : 0.551 12.786 41480 Z= 0.284 Chirality : 0.043 0.195 4616 Planarity : 0.004 0.079 5375 Dihedral : 4.247 25.623 4050 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.21 % Allowed : 15.11 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3733 helix: 0.75 (0.16), residues: 1030 sheet: -0.65 (0.18), residues: 736 loop : -1.02 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A 535 PHE 0.021 0.001 PHE D 106 TYR 0.017 0.001 TYR B 380 ARG 0.010 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1142) hydrogen bonds : angle 5.23450 ( 3177) SS BOND : bond 0.00379 ( 42) SS BOND : angle 2.11962 ( 84) covalent geometry : bond 0.00279 (30444) covalent geometry : angle 0.54337 (41396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 373 time to evaluate : 3.385 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 110 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.3871 (mp) REVERT: B 241 LEU cc_start: 0.7182 (mt) cc_final: 0.6954 (mp) REVERT: B 269 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6251 (p90) REVERT: B 393 THR cc_start: 0.8342 (p) cc_final: 0.8131 (t) REVERT: B 456 PHE cc_start: 0.6587 (m-80) cc_final: 0.6252 (m-80) REVERT: B 787 GLN cc_start: 0.8013 (pt0) cc_final: 0.7671 (pt0) REVERT: B 1142 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8355 (pp30) REVERT: C 191 GLU cc_start: 0.6323 (tt0) cc_final: 0.5856 (mt-10) REVERT: C 409 GLN cc_start: 0.1068 (mt0) cc_final: 0.0718 (pt0) REVERT: C 703 ASN cc_start: 0.8616 (t0) cc_final: 0.7640 (t0) REVERT: C 708 SER cc_start: 0.8342 (p) cc_final: 0.7850 (m) REVERT: C 904 TYR cc_start: 0.7460 (t80) cc_final: 0.6871 (t80) REVERT: C 1019 ARG cc_start: 0.8139 (tpt170) cc_final: 0.7894 (tpt170) REVERT: A 35 GLU cc_start: 0.7863 (mt-10) cc_final: 0.6637 (tp30) REVERT: A 82 MET cc_start: 0.6282 (mtt) cc_final: 0.5901 (mtm) REVERT: A 376 MET cc_start: 0.3308 (mtt) cc_final: 0.2838 (mpp) REVERT: A 400 PHE cc_start: 0.4663 (m-10) cc_final: 0.4434 (m-80) REVERT: A 482 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7413 (mtp85) REVERT: D 338 PHE cc_start: 0.6335 (p90) cc_final: 0.5918 (p90) REVERT: D 489 TYR cc_start: 0.6146 (t80) cc_final: 0.4170 (m-80) REVERT: D 516 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6381 (mp0) REVERT: D 751 ASN cc_start: 0.8794 (m-40) cc_final: 0.8542 (m110) REVERT: D 979 ASP cc_start: 0.8529 (m-30) cc_final: 0.7877 (t0) REVERT: D 1114 ILE cc_start: 0.9136 (mm) cc_final: 0.8730 (mm) outliers start: 73 outliers final: 48 residues processed: 427 average time/residue: 0.3998 time to fit residues: 282.8988 Evaluate side-chains 362 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 3.275 ------------------------------------------------------------------------------- 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 110 LEU 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 269 TYR Chi-restraints excluded: chain B residue 392 PHE 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 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 761 THR 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 275 PHE Chi-restraints excluded: chain C residue 278 LYS 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 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 133 CYS 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 66 HIS 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 336 CYS Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 588 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 36 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 362 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 703 ASN A 401 HIS D 957 GLN D 992 GLN D1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.157175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.128378 restraints weight = 84557.770| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.03 r_work: 0.3820 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30486 Z= 0.120 Angle : 0.537 12.232 41480 Z= 0.276 Chirality : 0.043 0.219 4616 Planarity : 0.004 0.066 5375 Dihedral : 4.137 25.400 4050 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.42 % Allowed : 15.48 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3733 helix: 0.96 (0.17), residues: 1028 sheet: -0.42 (0.18), residues: 743 loop : -0.97 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 566 HIS 0.004 0.001 HIS A 535 PHE 0.020 0.001 PHE C 823 TYR 0.015 0.001 TYR A 41 ARG 0.007 0.000 ARG C 815 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 1142) hydrogen bonds : angle 5.08131 ( 3177) SS BOND : bond 0.00413 ( 42) SS BOND : angle 1.94076 ( 84) covalent geometry : bond 0.00277 (30444) covalent geometry : angle 0.52989 (41396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 3.267 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 168 PHE cc_start: 0.6363 (t80) cc_final: 0.6073 (t80) REVERT: B 269 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.6181 (p90) REVERT: B 393 THR cc_start: 0.8326 (p) cc_final: 0.8093 (t) REVERT: B 456 PHE cc_start: 0.6437 (m-80) cc_final: 0.6106 (m-80) REVERT: B 787 GLN cc_start: 0.7951 (pt0) cc_final: 0.7592 (pt0) REVERT: B 1142 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8385 (pp30) REVERT: C 191 GLU cc_start: 0.6364 (tt0) cc_final: 0.5904 (mt-10) REVERT: C 336 CYS cc_start: 0.1979 (OUTLIER) cc_final: 0.0780 (t) REVERT: C 703 ASN cc_start: 0.8657 (t0) cc_final: 0.7733 (t0) REVERT: C 904 TYR cc_start: 0.7521 (t80) cc_final: 0.6942 (t80) REVERT: A 35 GLU cc_start: 0.7864 (mt-10) cc_final: 0.6587 (tp30) REVERT: A 82 MET cc_start: 0.6276 (mtt) cc_final: 0.5900 (mtm) REVERT: A 376 MET cc_start: 0.3416 (mtt) cc_final: 0.2962 (mpp) REVERT: A 400 PHE cc_start: 0.4602 (m-10) cc_final: 0.4208 (m-80) REVERT: A 482 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7366 (mtp85) REVERT: D 495 TYR cc_start: 0.4712 (m-80) cc_final: 0.4231 (m-80) REVERT: D 516 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6480 (mp0) REVERT: D 751 ASN cc_start: 0.8780 (m-40) cc_final: 0.8542 (m110) REVERT: D 896 ILE cc_start: 0.8200 (mm) cc_final: 0.7899 (mt) REVERT: D 979 ASP cc_start: 0.8475 (m-30) cc_final: 0.7894 (t0) outliers start: 80 outliers final: 58 residues processed: 400 average time/residue: 0.3708 time to fit residues: 244.8419 Evaluate side-chains 373 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 3.628 ------------------------------------------------------------------------------- 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 269 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE 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 534 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 761 THR 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 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 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 719 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 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 391 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 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 233 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 588 THR 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 1051 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 350 optimal weight: 4.9990 chunk 366 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 13 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 370 ASN B 613 GLN B 703 ASN B1005 GLN C 437 ASN C 709 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 76 GLN A 96 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS D 173 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.151064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.120736 restraints weight = 85125.475| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.06 r_work: 0.3727 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 30486 Z= 0.290 Angle : 0.727 13.411 41480 Z= 0.380 Chirality : 0.049 0.302 4616 Planarity : 0.005 0.066 5375 Dihedral : 5.275 26.312 4050 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.79 % Allowed : 15.57 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3733 helix: 0.33 (0.16), residues: 1023 sheet: -0.49 (0.19), residues: 713 loop : -1.27 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 48 HIS 0.006 0.002 HIS A 373 PHE 0.024 0.002 PHE C 643 TYR 0.028 0.002 TYR C 91 ARG 0.010 0.001 ARG D 815 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 1142) hydrogen bonds : angle 5.71627 ( 3177) SS BOND : bond 0.00699 ( 42) SS BOND : angle 2.33753 ( 84) covalent geometry : bond 0.00677 (30444) covalent geometry : angle 0.71965 (41396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 317 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 PHE cc_start: 0.6555 (t80) cc_final: 0.6051 (t80) REVERT: B 110 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4011 (mp) REVERT: B 456 PHE cc_start: 0.6469 (m-80) cc_final: 0.6025 (m-80) REVERT: B 787 GLN cc_start: 0.8335 (pt0) cc_final: 0.8054 (pt0) REVERT: B 1107 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6780 (tpt170) REVERT: C 336 CYS cc_start: 0.2379 (OUTLIER) cc_final: 0.1372 (t) REVERT: C 509 ARG cc_start: -0.3644 (OUTLIER) cc_final: -0.5761 (ptt90) REVERT: C 1029 MET cc_start: 0.8742 (tpp) cc_final: 0.8436 (ttm) REVERT: C 1050 MET cc_start: 0.8534 (ppp) cc_final: 0.8327 (ptt) REVERT: A 225 ASP cc_start: 0.3305 (OUTLIER) cc_final: 0.3013 (p0) REVERT: A 325 GLN cc_start: 0.7333 (tp40) cc_final: 0.5696 (pt0) REVERT: A 400 PHE cc_start: 0.5243 (m-80) cc_final: 0.4773 (m-80) REVERT: A 482 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7468 (mmt90) REVERT: D 473 TYR cc_start: 0.3895 (t80) cc_final: 0.3544 (t80) REVERT: D 495 TYR cc_start: 0.4886 (m-80) cc_final: 0.4519 (m-80) REVERT: D 954 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8324 (mt0) REVERT: D 979 ASP cc_start: 0.8576 (m-30) cc_final: 0.7928 (t0) outliers start: 125 outliers final: 86 residues processed: 405 average time/residue: 0.3924 time to fit residues: 264.3351 Evaluate side-chains 370 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 3.455 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 392 PHE 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 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 585 LEU 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 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP 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 275 PHE Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 603 ASN 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 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU 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 225 ASP Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 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 233 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 1051 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 129 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 182 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 301 optimal weight: 0.0670 chunk 184 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 314 GLN B 613 GLN B 703 ASN C 969 ASN A 524 GLN D 914 ASN D 957 GLN D1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.155933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.127744 restraints weight = 84949.490| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.00 r_work: 0.3810 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6064 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= 0.114 Angle : 0.550 12.347 41480 Z= 0.285 Chirality : 0.043 0.200 4616 Planarity : 0.004 0.061 5375 Dihedral : 4.457 28.204 4050 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.24 % Allowed : 17.63 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 3733 helix: 0.88 (0.17), residues: 1018 sheet: -0.40 (0.19), residues: 727 loop : -1.03 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.004 0.001 HIS A 535 PHE 0.021 0.001 PHE B 338 TYR 0.035 0.001 TYR A 41 ARG 0.007 0.000 ARG C 815 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 1142) hydrogen bonds : angle 5.15876 ( 3177) SS BOND : bond 0.00501 ( 42) SS BOND : angle 1.75975 ( 84) covalent geometry : bond 0.00259 (30444) covalent geometry : angle 0.54474 (41396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 3.179 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 168 PHE cc_start: 0.6564 (t80) cc_final: 0.6310 (t80) REVERT: B 269 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5991 (p90) REVERT: B 707 TYR cc_start: 0.3573 (OUTLIER) cc_final: 0.2733 (m-10) REVERT: B 1142 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8095 (pp30) REVERT: C 102 ARG cc_start: 0.7436 (mmt-90) cc_final: 0.7217 (mmt-90) REVERT: C 191 GLU cc_start: 0.7065 (tt0) cc_final: 0.6626 (tt0) REVERT: C 336 CYS cc_start: 0.2311 (OUTLIER) cc_final: 0.1100 (t) REVERT: C 904 TYR cc_start: 0.7591 (t80) cc_final: 0.7352 (t80) REVERT: C 1041 ASP cc_start: 0.8010 (m-30) cc_final: 0.7592 (m-30) REVERT: A 35 GLU cc_start: 0.7913 (mt-10) cc_final: 0.6551 (tm-30) REVERT: A 325 GLN cc_start: 0.7327 (tp40) cc_final: 0.5706 (pt0) REVERT: A 376 MET cc_start: 0.2957 (mmm) cc_final: 0.2731 (mmm) REVERT: A 400 PHE cc_start: 0.5144 (m-10) cc_final: 0.3840 (m-80) REVERT: D 495 TYR cc_start: 0.4964 (m-80) cc_final: 0.4208 (m-80) REVERT: D 751 ASN cc_start: 0.8804 (m-40) cc_final: 0.8573 (m110) REVERT: D 979 ASP cc_start: 0.8407 (m-30) cc_final: 0.7961 (t0) REVERT: D 1072 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7521 (mt-10) outliers start: 74 outliers final: 54 residues processed: 384 average time/residue: 0.3853 time to fit residues: 243.6605 Evaluate side-chains 353 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 295 time to evaluate : 3.580 ------------------------------------------------------------------------------- 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 269 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP 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 336 CYS Chi-restraints excluded: chain C residue 656 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 747 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 223 ILE 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 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 66 HIS 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 284 THR Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 645 THR 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 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 151 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 335 optimal weight: 0.0870 chunk 257 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN C 422 ASN C 703 ASN C 751 ASN C 969 ASN C1142 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.155638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.127887 restraints weight = 84414.072| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.89 r_work: 0.3819 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30486 Z= 0.116 Angle : 0.541 11.982 41480 Z= 0.278 Chirality : 0.043 0.169 4616 Planarity : 0.004 0.059 5375 Dihedral : 4.303 26.550 4050 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.57 % Allowed : 17.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3733 helix: 1.11 (0.17), residues: 1007 sheet: -0.30 (0.19), residues: 753 loop : -0.95 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.022 0.001 PHE D 541 TYR 0.029 0.001 TYR A 41 ARG 0.007 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 1142) hydrogen bonds : angle 5.03220 ( 3177) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.56492 ( 84) covalent geometry : bond 0.00267 (30444) covalent geometry : angle 0.53723 (41396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 320 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5939 (p90) REVERT: B 456 PHE cc_start: 0.6233 (m-80) cc_final: 0.6007 (m-10) REVERT: B 787 GLN cc_start: 0.7845 (pt0) cc_final: 0.7397 (pt0) REVERT: C 191 GLU cc_start: 0.7172 (tt0) cc_final: 0.6680 (tp30) REVERT: C 336 CYS cc_start: 0.2282 (OUTLIER) cc_final: 0.1089 (t) REVERT: C 904 TYR cc_start: 0.7596 (t80) cc_final: 0.7334 (t80) REVERT: C 1041 ASP cc_start: 0.7997 (m-30) cc_final: 0.7576 (m-30) REVERT: A 35 GLU cc_start: 0.7892 (mt-10) cc_final: 0.6546 (tp30) REVERT: A 325 GLN cc_start: 0.7121 (tp40) cc_final: 0.5715 (pt0) REVERT: A 376 MET cc_start: 0.3151 (mmm) cc_final: 0.2911 (mmm) REVERT: A 400 PHE cc_start: 0.5234 (m-10) cc_final: 0.3893 (m-80) REVERT: A 442 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6501 (tm-30) REVERT: D 495 TYR cc_start: 0.5062 (m-80) cc_final: 0.4328 (m-80) REVERT: D 516 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6732 (mp0) REVERT: D 751 ASN cc_start: 0.8805 (m-40) cc_final: 0.8568 (m110) REVERT: D 979 ASP cc_start: 0.8344 (m-30) cc_final: 0.7906 (t0) REVERT: D 1072 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7509 (mt-10) outliers start: 85 outliers final: 64 residues processed: 386 average time/residue: 0.4255 time to fit residues: 274.5680 Evaluate side-chains 367 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 5.300 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 269 TYR 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 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 552 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 585 LEU 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 884 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 239 GLN 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 441 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 708 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER 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 133 CYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 285 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 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 66 HIS Chi-restraints excluded: chain D residue 120 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 336 CYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 77 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 913 GLN C 969 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.153674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.125815 restraints weight = 84262.906| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.65 r_work: 0.3790 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30486 Z= 0.153 Angle : 0.583 11.855 41480 Z= 0.299 Chirality : 0.044 0.159 4616 Planarity : 0.004 0.054 5375 Dihedral : 4.492 27.776 4050 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.30 % Allowed : 18.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3733 helix: 1.04 (0.17), residues: 1007 sheet: -0.27 (0.18), residues: 761 loop : -0.99 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.005 0.001 HIS A 374 PHE 0.020 0.002 PHE B 562 TYR 0.023 0.002 TYR A 41 ARG 0.007 0.001 ARG C 815 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1142) hydrogen bonds : angle 5.15209 ( 3177) SS BOND : bond 0.00466 ( 42) SS BOND : angle 1.87332 ( 84) covalent geometry : bond 0.00357 (30444) covalent geometry : angle 0.57754 (41396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 304 time to evaluate : 3.600 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 269 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6386 (p90) REVERT: B 338 PHE cc_start: 0.6614 (m-10) cc_final: 0.5411 (p90) REVERT: B 456 PHE cc_start: 0.6220 (m-80) cc_final: 0.5826 (m-80) REVERT: B 787 GLN cc_start: 0.8175 (pt0) cc_final: 0.7970 (pt0) REVERT: C 703 ASN cc_start: 0.8916 (t0) cc_final: 0.8292 (t0) REVERT: C 1019 ARG cc_start: 0.8218 (tpt170) cc_final: 0.7940 (tpm170) REVERT: C 1029 MET cc_start: 0.8918 (tpp) cc_final: 0.8603 (ttm) REVERT: C 1041 ASP cc_start: 0.8200 (m-30) cc_final: 0.7871 (m-30) REVERT: A 35 GLU cc_start: 0.7922 (mt-10) cc_final: 0.6502 (tm-30) REVERT: A 325 GLN cc_start: 0.7396 (tp40) cc_final: 0.5935 (pt0) REVERT: A 376 MET cc_start: 0.3183 (mmm) cc_final: 0.2848 (mmm) REVERT: A 400 PHE cc_start: 0.5417 (m-10) cc_final: 0.4020 (m-80) REVERT: D 495 TYR cc_start: 0.5071 (m-80) cc_final: 0.4457 (m-80) REVERT: D 751 ASN cc_start: 0.8835 (m-40) cc_final: 0.8562 (m110) REVERT: D 979 ASP cc_start: 0.8488 (m-30) cc_final: 0.8073 (t0) REVERT: D 1072 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7747 (mt-10) outliers start: 76 outliers final: 68 residues processed: 361 average time/residue: 0.3755 time to fit residues: 226.1175 Evaluate side-chains 365 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 295 time to evaluate : 3.361 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 269 TYR 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 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 552 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 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 171 VAL Chi-restraints excluded: chain C residue 239 GLN 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 441 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 708 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER 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 223 ILE Chi-restraints excluded: chain A residue 285 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 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 66 HIS Chi-restraints excluded: chain D residue 120 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 336 CYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 266 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 107 optimal weight: 0.0570 chunk 151 optimal weight: 0.7980 chunk 370 optimal weight: 0.6980 chunk 290 optimal weight: 0.0010 chunk 224 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 969 ASN A 34 HIS D 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.157112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.128113 restraints weight = 84280.830| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 3.24 r_work: 0.3814 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 30486 Z= 0.101 Angle : 0.536 11.896 41480 Z= 0.274 Chirality : 0.043 0.186 4616 Planarity : 0.003 0.051 5375 Dihedral : 4.116 25.335 4050 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.79 % Allowed : 18.81 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3733 helix: 1.27 (0.17), residues: 1015 sheet: -0.20 (0.19), residues: 749 loop : -0.89 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 886 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE B 338 TYR 0.023 0.001 TYR A 41 ARG 0.007 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1142) hydrogen bonds : angle 4.94380 ( 3177) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.78925 ( 84) covalent geometry : bond 0.00227 (30444) covalent geometry : angle 0.53067 (41396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7466 Ramachandran restraints generated. 3733 Oldfield, 0 Emsley, 3733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 320 time to evaluate : 3.325 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 269 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.5962 (p90) REVERT: B 338 PHE cc_start: 0.6527 (m-10) cc_final: 0.5427 (p90) REVERT: B 456 PHE cc_start: 0.6254 (m-80) cc_final: 0.5968 (m-80) REVERT: B 787 GLN cc_start: 0.7790 (pt0) cc_final: 0.7450 (pt0) REVERT: C 191 GLU cc_start: 0.7258 (tt0) cc_final: 0.6806 (tt0) REVERT: C 336 CYS cc_start: 0.2271 (OUTLIER) cc_final: 0.1017 (t) REVERT: C 904 TYR cc_start: 0.7471 (t80) cc_final: 0.7245 (t80) REVERT: C 1019 ARG cc_start: 0.8059 (tpt170) cc_final: 0.7834 (tpm170) REVERT: C 1041 ASP cc_start: 0.7915 (m-30) cc_final: 0.7526 (m-30) REVERT: A 35 GLU cc_start: 0.7902 (mt-10) cc_final: 0.6536 (tp30) REVERT: A 325 GLN cc_start: 0.7311 (tp40) cc_final: 0.5936 (pt0) REVERT: A 376 MET cc_start: 0.3085 (mmm) cc_final: 0.2750 (mmm) REVERT: A 400 PHE cc_start: 0.5648 (m-10) cc_final: 0.4113 (m-80) REVERT: A 442 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6383 (tm-30) REVERT: A 482 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7162 (mtp85) REVERT: D 495 TYR cc_start: 0.5106 (m-80) cc_final: 0.4378 (m-80) REVERT: D 516 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6609 (mp0) REVERT: D 751 ASN cc_start: 0.8676 (m-40) cc_final: 0.8475 (m110) REVERT: D 979 ASP cc_start: 0.8207 (m-30) cc_final: 0.7897 (t0) REVERT: D 1072 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: D 1114 ILE cc_start: 0.9025 (mm) cc_final: 0.8577 (mm) outliers start: 59 outliers final: 48 residues processed: 363 average time/residue: 0.3856 time to fit residues: 233.7651 Evaluate side-chains 351 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 300 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain B residue 269 TYR 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 539 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 707 TYR 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 239 GLN 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 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 248 LEU 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 579 MET Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 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 721 SER Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 1051 SER Chi-restraints excluded: chain D residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 366 optimal weight: 0.1980 chunk 292 optimal weight: 0.0870 chunk 152 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 354 optimal weight: 2.9990 chunk 376 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 350 optimal weight: 0.2980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 856 ASN C1071 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 = 0.4405 r_free = 0.4405 target = 0.157170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.128506 restraints weight = 84722.510| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.04 r_work: 0.3842 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 30486 Z= 0.099 Angle : 0.537 14.227 41480 Z= 0.273 Chirality : 0.043 0.163 4616 Planarity : 0.003 0.050 5375 Dihedral : 3.989 23.115 4050 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 19.20 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3733 helix: 1.37 (0.17), residues: 1021 sheet: -0.07 (0.19), residues: 742 loop : -0.84 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 886 HIS 0.004 0.001 HIS A 374 PHE 0.026 0.001 PHE D 135 TYR 0.022 0.001 TYR A 41 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 1142) hydrogen bonds : angle 4.83506 ( 3177) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.58111 ( 84) covalent geometry : bond 0.00220 (30444) covalent geometry : angle 0.53263 (41396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20107.94 seconds wall clock time: 353 minutes 48.04 seconds (21228.04 seconds total)