Starting phenix.real_space_refine on Tue May 27 23:08:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wro_37784/05_2025/8wro_37784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wro_37784/05_2025/8wro_37784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wro_37784/05_2025/8wro_37784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wro_37784/05_2025/8wro_37784.map" model { file = "/net/cci-nas-00/data/ceres_data/8wro_37784/05_2025/8wro_37784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wro_37784/05_2025/8wro_37784.cif" } resolution = 3.9 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= -0.000 sd= 0.045 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 146 5.16 5 C 19060 2.51 5 N 4969 2.21 5 O 5632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29807 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8364 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8295 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 57, 'TRANS': 1001} Chain breaks: 5 Chain: "C" Number of atoms: 8303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8303 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 57, 'TRANS': 1002} Chain breaks: 5 Chain: "D" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 16.57, per 1000 atoms: 0.56 Number of scatterers: 29807 At special positions: 0 Unit cell: (151.84, 164.32, 236.08, 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 146 16.00 O 5632 8.00 N 4969 7.00 C 19060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.02 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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: 7.32 Conformation dependent library (CDL) restraints added in 3.5 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7100 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 48 sheets defined 28.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.785A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE A 368 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.541A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 775 removed outlier: 4.312A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 938 removed outlier: 4.075A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 3.548A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.934A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 3.650A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1030 removed outlier: 3.601A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.521A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.952A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.536A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 774 removed outlier: 3.694A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.781A pdb=" N ASN B 853 " --> pdb=" O GLN B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.564A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.598A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.907A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.685A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 5.074A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.958A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.061A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.738A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.666A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.508A pdb=" N LYS C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN C 776 " --> pdb=" O ASP C 772 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 777 " --> pdb=" O LYS C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.638A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.704A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.939A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.734A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 961 removed outlier: 4.621A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 951 " --> pdb=" O ASP C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 965 Processing helix chain 'C' and resid 973 through 980 removed outlier: 3.809A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 985 Processing helix chain 'C' and resid 986 through 1030 removed outlier: 4.078A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.670A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.615A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.607A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.779A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.597A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.781A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 268 removed outlier: 3.988A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 331 removed outlier: 4.517A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.513A pdb=" N PHE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 412 removed outlier: 4.252A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.487A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.933A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.564A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 597 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.887A pdb=" N ASP A 50 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 270 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.988A pdb=" N THR A 60 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 264 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 262 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 200 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 224 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 128 removed outlier: 3.938A pdb=" N TRP A 101 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.745A pdb=" N GLY A 308 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 596 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 325 removed outlier: 3.717A pdb=" N VAL A 536 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.864A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A 427 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.864A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A 427 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 431 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.238A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700 Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.851A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.851A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 732 removed outlier: 4.794A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1117 through 1120 Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.207A pdb=" N LEU B 81 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 234 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 103 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN B 236 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP B 101 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 238 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 123 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 169 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 125 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.455A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.966A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 324 removed outlier: 7.012A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 536 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.609A pdb=" N GLY B 428 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.652A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.706A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.773A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.647A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.703A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD3, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.437A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 26 through 27 removed outlier: 4.019A pdb=" N THR C 26 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 59 " --> pdb=" O THR C 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 46 through 52 removed outlier: 3.803A pdb=" N HIS C 46 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 274 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 48 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.960A pdb=" N LEU C 81 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN C 236 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP C 101 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 238 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.998A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 224 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.515A pdb=" N GLY C 308 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 647 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AE1, first strand: chain 'C' and resid 395 through 400 removed outlier: 4.122A pdb=" N ILE C 399 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 548 through 551 Processing sheet with id=AE4, first strand: chain 'C' and resid 661 through 662 removed outlier: 3.760A pdb=" N ILE C 661 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 716 removed outlier: 3.500A pdb=" N THR C 720 " --> pdb=" O HIS C1061 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 716 removed outlier: 6.058A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.481A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C1078 " --> pdb=" O HIS C1085 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.647A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.452A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.494A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2931 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: 14.66 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: 1.21 - 1.33: 8551 1.33 - 1.46: 8066 1.46 - 1.59: 13729 1.59 - 1.71: 1 1.71 - 1.84: 197 Bond restraints: 30544 Sorted by residual: bond pdb=" C PRO C 983 " pdb=" O PRO C 983 " ideal model delta sigma weight residual 1.240 1.208 0.032 1.12e-02 7.97e+03 8.17e+00 bond pdb=" N GLU C 985 " pdb=" CA GLU C 985 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.43e+00 bond pdb=" CB PRO C 334 " pdb=" CG PRO C 334 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" N ARG C 980 " pdb=" CA ARG C 980 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.70e+00 bond pdb=" N ASP C 982 " pdb=" CA ASP C 982 " ideal model delta sigma weight residual 1.451 1.487 -0.037 1.78e-02 3.16e+03 4.23e+00 ... (remaining 30539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 41156 3.13 - 6.25: 322 6.25 - 9.38: 70 9.38 - 12.51: 10 12.51 - 15.63: 2 Bond angle restraints: 41560 Sorted by residual: angle pdb=" CG1 ILE B 19 " pdb=" CB ILE B 19 " pdb=" CG2 ILE B 19 " ideal model delta sigma weight residual 110.70 95.07 15.63 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C GLU D 479 " pdb=" N MET D 480 " pdb=" CA MET D 480 " ideal model delta sigma weight residual 122.06 112.47 9.59 1.86e+00 2.89e-01 2.66e+01 angle pdb=" CB MET B 694 " pdb=" CG MET B 694 " pdb=" SD MET B 694 " ideal model delta sigma weight residual 112.70 127.22 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA MET A 150 " pdb=" CB MET A 150 " pdb=" CG MET A 150 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA PRO C 334 " pdb=" N PRO C 334 " pdb=" CD PRO C 334 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.21e+01 ... (remaining 41555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15311 18.00 - 36.00: 2114 36.00 - 53.99: 592 53.99 - 71.99: 123 71.99 - 89.99: 59 Dihedral angle restraints: 18199 sinusoidal: 7166 harmonic: 11033 Sorted by residual: dihedral pdb=" CB CYS C 735 " pdb=" SG CYS C 735 " pdb=" SG CYS C 757 " pdb=" CB CYS C 757 " ideal model delta sinusoidal sigma weight residual -86.00 0.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 133 " pdb=" CB CYS C 133 " ideal model delta sinusoidal sigma weight residual 93.00 171.74 -78.74 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -162.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 ... (remaining 18196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4139 0.081 - 0.163: 475 0.163 - 0.244: 16 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 4633 Sorted by residual: chirality pdb=" CB ILE B 19 " pdb=" CA ILE B 19 " pdb=" CG1 ILE B 19 " pdb=" CG2 ILE B 19 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE A 98 " pdb=" CA ILE A 98 " pdb=" CG1 ILE A 98 " pdb=" CG2 ILE A 98 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU C 81 " pdb=" CB LEU C 81 " pdb=" CD1 LEU C 81 " pdb=" CD2 LEU C 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4630 not shown) Planarity restraints: 5380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 980 " 0.415 9.50e-02 1.11e+02 1.86e-01 2.12e+01 pdb=" NE ARG C 980 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG C 980 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 980 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 980 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.024 2.00e-02 2.50e+03 1.95e-02 9.47e+00 pdb=" CG TRP D 461 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 982 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO A 983 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.040 5.00e-02 4.00e+02 ... (remaining 5377 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5778 2.77 - 3.30: 28495 3.30 - 3.83: 51396 3.83 - 4.37: 54580 4.37 - 4.90: 93629 Nonbonded interactions: 233878 Sorted by model distance: nonbonded pdb=" O ASP A 933 " pdb=" OG SER A 937 " model vdw 2.237 3.040 nonbonded pdb=" O TYR C 310 " pdb=" OG SER C 593 " model vdw 2.243 3.040 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.258 3.040 nonbonded pdb=" O SER A 964 " pdb=" OG SER A 964 " model vdw 2.269 3.040 nonbonded pdb=" O SER A 24 " pdb=" OG1 THR A 60 " model vdw 2.277 3.040 ... (remaining 233873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 140 or resid 149 through 824 or resid 847 throu \ gh 1137)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 824 or resid 847 through 1137)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 1.290 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 67.850 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 0.110 30584 Z= 0.192 Angle : 0.792 15.632 41640 Z= 0.413 Chirality : 0.049 0.407 4633 Planarity : 0.006 0.186 5380 Dihedral : 18.348 89.988 10979 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 0.33 % Allowed : 34.33 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.13), residues: 3742 helix: 0.45 (0.16), residues: 956 sheet: -1.36 (0.20), residues: 616 loop : -2.33 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 461 HIS 0.009 0.001 HIS C 336 PHE 0.036 0.002 PHE C 397 TYR 0.024 0.001 TYR C 362 ARG 0.006 0.000 ARG C1104 Details of bonding type rmsd hydrogen bonds : bond 0.14112 ( 1019) hydrogen bonds : angle 6.25269 ( 2931) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.35246 ( 80) covalent geometry : bond 0.00407 (30544) covalent geometry : angle 0.79090 (41560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 464 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7816 (ttpt) REVERT: A 89 PHE cc_start: 0.8432 (t80) cc_final: 0.8001 (t80) REVERT: A 492 TYR cc_start: 0.1387 (OUTLIER) cc_final: 0.0988 (m-80) REVERT: A 694 MET cc_start: 0.7386 (mmt) cc_final: 0.7085 (tpt) REVERT: A 752 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8525 (mp10) REVERT: A 897 MET cc_start: 0.7268 (tpp) cc_final: 0.6933 (tpp) REVERT: A 987 GLU cc_start: 0.8359 (mp0) cc_final: 0.7899 (mp0) REVERT: B 272 PHE cc_start: 0.7340 (m-80) cc_final: 0.6543 (t80) REVERT: B 694 MET cc_start: 0.7498 (mmm) cc_final: 0.7104 (mmm) REVERT: B 737 MET cc_start: 0.7160 (tpp) cc_final: 0.6934 (mmm) REVERT: B 744 THR cc_start: 0.8649 (t) cc_final: 0.8116 (t) REVERT: B 748 ASN cc_start: 0.8940 (m110) cc_final: 0.8042 (m-40) REVERT: B 756 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 1046 LEU cc_start: 0.8415 (mt) cc_final: 0.7902 (tt) REVERT: B 1122 ASN cc_start: 0.6135 (p0) cc_final: 0.5789 (p0) REVERT: C 81 LEU cc_start: 0.8063 (tt) cc_final: 0.7105 (mm) REVERT: C 89 PHE cc_start: 0.7108 (t80) cc_final: 0.6513 (t80) REVERT: C 122 ASN cc_start: 0.8001 (m-40) cc_final: 0.7213 (p0) REVERT: C 392 VAL cc_start: 0.7276 (p) cc_final: 0.6971 (m) REVERT: C 420 TYR cc_start: 0.6532 (t80) cc_final: 0.6321 (t80) REVERT: C 539 ASN cc_start: 0.7935 (t0) cc_final: 0.7305 (p0) REVERT: C 870 TYR cc_start: 0.6829 (m-80) cc_final: 0.6502 (m-80) REVERT: C 884 THR cc_start: 0.7886 (p) cc_final: 0.7674 (t) REVERT: D 107 VAL cc_start: 0.7224 (t) cc_final: 0.6834 (t) REVERT: D 295 ASP cc_start: 0.8685 (t0) cc_final: 0.8344 (p0) REVERT: D 577 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8228 (tptt) outliers start: 11 outliers final: 3 residues processed: 472 average time/residue: 0.3817 time to fit residues: 294.0892 Evaluate side-chains 261 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 256 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain C residue 648 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 50.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 ASN B 474 ASN ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN B 910 GLN C 131 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN D 61 ASN D 188 ASN D 250 ASN D 429 GLN D 586 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.117714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.097737 restraints weight = 168305.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.096450 restraints weight = 122595.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.096668 restraints weight = 96762.136| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30584 Z= 0.133 Angle : 0.630 9.602 41640 Z= 0.323 Chirality : 0.044 0.211 4633 Planarity : 0.005 0.072 5380 Dihedral : 4.848 46.926 4067 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.32 % Rotamer: Outliers : 3.98 % Allowed : 32.28 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.13), residues: 3742 helix: 1.04 (0.17), residues: 971 sheet: -1.26 (0.21), residues: 618 loop : -2.15 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 461 HIS 0.013 0.001 HIS A1080 PHE 0.029 0.001 PHE B 189 TYR 0.022 0.002 TYR C 914 ARG 0.011 0.001 ARG C 495 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1019) hydrogen bonds : angle 5.09787 ( 2931) SS BOND : bond 0.00221 ( 40) SS BOND : angle 1.28081 ( 80) covalent geometry : bond 0.00294 (30544) covalent geometry : angle 0.62763 (41560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 271 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7865 (mm) cc_final: 0.7173 (tp) REVERT: A 321 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: A 402 ASN cc_start: 0.4206 (OUTLIER) cc_final: 0.3406 (p0) REVERT: A 752 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8158 (mp10) REVERT: A 1027 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8116 (t) REVERT: B 98 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5654 (tt) REVERT: B 187 ARG cc_start: 0.6682 (mtt180) cc_final: 0.6244 (mtt180) REVERT: B 272 PHE cc_start: 0.7083 (m-80) cc_final: 0.6465 (t80) REVERT: B 293 LEU cc_start: 0.8227 (tp) cc_final: 0.7952 (tt) REVERT: B 744 THR cc_start: 0.8691 (t) cc_final: 0.8072 (t) REVERT: B 748 ASN cc_start: 0.8857 (m110) cc_final: 0.8180 (m-40) REVERT: B 1046 LEU cc_start: 0.8369 (mt) cc_final: 0.8023 (tt) REVERT: C 81 LEU cc_start: 0.7503 (tt) cc_final: 0.6976 (mm) REVERT: C 122 ASN cc_start: 0.7915 (m-40) cc_final: 0.7137 (p0) REVERT: C 539 ASN cc_start: 0.7749 (t0) cc_final: 0.7091 (p0) REVERT: C 728 MET cc_start: 0.8785 (ppp) cc_final: 0.7322 (ppp) REVERT: C 982 ASP cc_start: 0.8033 (p0) cc_final: 0.7699 (p0) REVERT: D 74 LYS cc_start: 0.5704 (tptt) cc_final: 0.4784 (tptt) REVERT: D 192 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7671 (tpm170) REVERT: D 295 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8105 (p0) REVERT: D 332 MET cc_start: -0.1057 (tmm) cc_final: -0.2566 (ptp) REVERT: D 427 ASP cc_start: 0.5496 (OUTLIER) cc_final: 0.5253 (m-30) REVERT: D 480 MET cc_start: 0.1001 (OUTLIER) cc_final: 0.0799 (ttp) REVERT: D 506 VAL cc_start: 0.3731 (OUTLIER) cc_final: 0.3338 (p) outliers start: 132 outliers final: 49 residues processed: 386 average time/residue: 0.3721 time to fit residues: 237.5886 Evaluate side-chains 279 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 853 ASN Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1135 TYR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 91 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 238 optimal weight: 0.1980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 131 GLN B 474 ASN ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 748 ASN B 917 GLN B1007 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1085 HIS C 46 HIS C 66 HIS ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 898 GLN C1055 HIS D 580 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.115049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.094037 restraints weight = 166060.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.092011 restraints weight = 103751.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.092625 restraints weight = 89369.029| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30584 Z= 0.132 Angle : 0.601 10.348 41640 Z= 0.304 Chirality : 0.043 0.175 4633 Planarity : 0.005 0.061 5380 Dihedral : 4.521 23.694 4060 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.71 % Favored : 93.21 % Rotamer: Outliers : 4.10 % Allowed : 31.89 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.14), residues: 3742 helix: 1.23 (0.17), residues: 976 sheet: -1.23 (0.21), residues: 579 loop : -2.08 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 477 HIS 0.014 0.001 HIS C 46 PHE 0.024 0.001 PHE B 397 TYR 0.040 0.001 TYR B 348 ARG 0.009 0.000 ARG C 902 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 1019) hydrogen bonds : angle 4.86367 ( 2931) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.03951 ( 80) covalent geometry : bond 0.00283 (30544) covalent geometry : angle 0.59994 (41560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 245 time to evaluate : 3.398 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: A 51 LEU cc_start: 0.7877 (mm) cc_final: 0.7203 (tp) REVERT: A 402 ASN cc_start: 0.4254 (OUTLIER) cc_final: 0.3406 (p0) REVERT: A 1125 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 150 MET cc_start: 0.6313 (mmp) cc_final: 0.6042 (mmt) REVERT: B 187 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6598 (mtt180) REVERT: B 272 PHE cc_start: 0.7149 (m-80) cc_final: 0.6721 (t80) REVERT: B 293 LEU cc_start: 0.8260 (tp) cc_final: 0.8028 (tt) REVERT: B 477 CYS cc_start: -0.0427 (OUTLIER) cc_final: -0.3575 (p) REVERT: B 744 THR cc_start: 0.8503 (t) cc_final: 0.8217 (t) REVERT: B 748 ASN cc_start: 0.8839 (m-40) cc_final: 0.8463 (m-40) REVERT: B 897 MET cc_start: 0.8340 (tpp) cc_final: 0.8065 (tpp) REVERT: C 81 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7136 (mm) REVERT: C 89 PHE cc_start: 0.7125 (t80) cc_final: 0.6912 (t80) REVERT: C 122 ASN cc_start: 0.8032 (m-40) cc_final: 0.7204 (p0) REVERT: C 189 PHE cc_start: 0.6879 (m-80) cc_final: 0.6414 (m-10) REVERT: C 239 LEU cc_start: 0.8103 (mt) cc_final: 0.7894 (pt) REVERT: C 389 PHE cc_start: 0.7670 (m-80) cc_final: 0.7459 (m-80) REVERT: C 539 ASN cc_start: 0.7757 (t0) cc_final: 0.7027 (p0) REVERT: C 728 MET cc_start: 0.8624 (ppp) cc_final: 0.7010 (ppp) REVERT: D 82 MET cc_start: 0.4417 (ppp) cc_final: 0.4080 (ppp) REVERT: D 192 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7653 (tpm170) REVERT: D 295 ASP cc_start: 0.8636 (t0) cc_final: 0.8085 (p0) REVERT: D 318 VAL cc_start: 0.2945 (t) cc_final: 0.2662 (t) REVERT: D 364 VAL cc_start: -0.1948 (OUTLIER) cc_final: -0.2906 (t) REVERT: D 480 MET cc_start: 0.1483 (OUTLIER) cc_final: 0.1185 (ppp) REVERT: D 506 VAL cc_start: 0.3513 (OUTLIER) cc_final: 0.3165 (p) outliers start: 136 outliers final: 69 residues processed: 365 average time/residue: 0.3460 time to fit residues: 211.6767 Evaluate side-chains 280 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 168 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 419 ASN A 471 GLN A 954 GLN B 474 ASN B 502 HIS B 892 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN C 641 GLN C 898 GLN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 580 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.109243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.081976 restraints weight = 160053.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081894 restraints weight = 107728.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.082254 restraints weight = 71122.420| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30584 Z= 0.192 Angle : 0.638 13.836 41640 Z= 0.328 Chirality : 0.044 0.197 4633 Planarity : 0.005 0.068 5380 Dihedral : 4.666 27.218 4060 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 5.43 % Allowed : 31.64 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.14), residues: 3742 helix: 1.12 (0.17), residues: 988 sheet: -1.28 (0.22), residues: 554 loop : -2.05 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 461 HIS 0.010 0.001 HIS D 239 PHE 0.020 0.002 PHE B 397 TYR 0.043 0.002 TYR C 262 ARG 0.016 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1019) hydrogen bonds : angle 4.97460 ( 2931) SS BOND : bond 0.00378 ( 40) SS BOND : angle 1.22281 ( 80) covalent geometry : bond 0.00417 (30544) covalent geometry : angle 0.63610 (41560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 205 time to evaluate : 3.426 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: A 51 LEU cc_start: 0.8019 (mm) cc_final: 0.7316 (tp) REVERT: A 402 ASN cc_start: 0.4317 (OUTLIER) cc_final: 0.3332 (p0) REVERT: A 471 GLN cc_start: 0.4522 (OUTLIER) cc_final: 0.4007 (tm-30) REVERT: B 187 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7253 (mtt180) REVERT: B 198 PHE cc_start: 0.7571 (m-80) cc_final: 0.7040 (m-80) REVERT: B 272 PHE cc_start: 0.7422 (m-80) cc_final: 0.6951 (t80) REVERT: B 477 CYS cc_start: 0.1043 (OUTLIER) cc_final: -0.2388 (p) REVERT: B 722 GLU cc_start: 0.8576 (pm20) cc_final: 0.8296 (pm20) REVERT: B 730 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8847 (mtmt) REVERT: B 744 THR cc_start: 0.8589 (t) cc_final: 0.8367 (t) REVERT: B 748 ASN cc_start: 0.8919 (m-40) cc_final: 0.8676 (m-40) REVERT: B 792 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6898 (mmtm) REVERT: C 81 LEU cc_start: 0.7764 (tt) cc_final: 0.7370 (mm) REVERT: C 239 LEU cc_start: 0.8324 (mt) cc_final: 0.7910 (pt) REVERT: C 339 PHE cc_start: 0.2485 (OUTLIER) cc_final: 0.2023 (t80) REVERT: C 389 PHE cc_start: 0.7863 (m-80) cc_final: 0.7591 (m-80) REVERT: C 728 MET cc_start: 0.8879 (ppp) cc_final: 0.7347 (ppp) REVERT: C 748 ASN cc_start: 0.8560 (m110) cc_final: 0.8305 (m-40) REVERT: C 773 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8576 (tttm) REVERT: C 1038 ASP cc_start: 0.6636 (t0) cc_final: 0.6405 (t0) REVERT: D 74 LYS cc_start: 0.6337 (tptt) cc_final: 0.5308 (tptt) REVERT: D 82 MET cc_start: 0.4105 (ppp) cc_final: 0.3833 (ppp) REVERT: D 192 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7713 (tpm170) REVERT: D 295 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8182 (p0) REVERT: D 480 MET cc_start: 0.0897 (OUTLIER) cc_final: 0.0152 (ttp) REVERT: D 506 VAL cc_start: 0.3598 (OUTLIER) cc_final: 0.3246 (p) outliers start: 180 outliers final: 92 residues processed: 371 average time/residue: 0.3614 time to fit residues: 225.3465 Evaluate side-chains 278 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 176 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 580 ASN Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 174 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 240 optimal weight: 20.0000 chunk 336 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 368 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 484 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 539 ASN ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN D 154 ASN D 388 GLN D 556 ASN D 580 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.107750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.081623 restraints weight = 154400.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.080154 restraints weight = 109459.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.080236 restraints weight = 84492.282| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30584 Z= 0.154 Angle : 0.611 9.863 41640 Z= 0.309 Chirality : 0.043 0.169 4633 Planarity : 0.004 0.058 5380 Dihedral : 4.570 26.227 4060 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.81 % Favored : 93.08 % Rotamer: Outliers : 4.16 % Allowed : 32.34 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.14), residues: 3742 helix: 1.24 (0.17), residues: 989 sheet: -1.31 (0.20), residues: 605 loop : -2.04 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 461 HIS 0.008 0.001 HIS C 336 PHE 0.022 0.001 PHE B 397 TYR 0.030 0.001 TYR C 262 ARG 0.005 0.001 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 1019) hydrogen bonds : angle 4.83916 ( 2931) SS BOND : bond 0.00515 ( 40) SS BOND : angle 0.97943 ( 80) covalent geometry : bond 0.00346 (30544) covalent geometry : angle 0.61057 (41560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 182 time to evaluate : 3.694 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: A 51 LEU cc_start: 0.7941 (mm) cc_final: 0.7365 (tp) REVERT: A 174 MET cc_start: -0.0003 (tpt) cc_final: -0.0320 (tpp) REVERT: A 402 ASN cc_start: 0.3991 (OUTLIER) cc_final: 0.2946 (p0) REVERT: B 150 MET cc_start: 0.6627 (mmp) cc_final: 0.6307 (mmt) REVERT: B 198 PHE cc_start: 0.7514 (m-80) cc_final: 0.7296 (m-80) REVERT: B 477 CYS cc_start: 0.0918 (OUTLIER) cc_final: -0.2766 (p) REVERT: B 722 GLU cc_start: 0.8622 (pm20) cc_final: 0.8266 (pm20) REVERT: B 744 THR cc_start: 0.8371 (t) cc_final: 0.8160 (t) REVERT: B 792 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7012 (mmtm) REVERT: C 81 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7486 (mm) REVERT: C 101 TRP cc_start: 0.4846 (m-10) cc_final: 0.4528 (m-90) REVERT: C 221 GLU cc_start: 0.6846 (tp30) cc_final: 0.6341 (tp30) REVERT: C 339 PHE cc_start: 0.2734 (OUTLIER) cc_final: 0.2414 (t80) REVERT: C 539 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: C 641 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6969 (tp-100) REVERT: C 728 MET cc_start: 0.8909 (ppp) cc_final: 0.7435 (ppp) REVERT: C 748 ASN cc_start: 0.8493 (m110) cc_final: 0.8263 (m110) REVERT: D 74 LYS cc_start: 0.6187 (tptt) cc_final: 0.5150 (tptt) REVERT: D 82 MET cc_start: 0.3914 (ppp) cc_final: 0.3634 (ppp) REVERT: D 192 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7636 (tpm170) REVERT: D 295 ASP cc_start: 0.8591 (t0) cc_final: 0.8096 (p0) REVERT: D 332 MET cc_start: -0.1854 (tmm) cc_final: -0.2681 (ptm) REVERT: D 480 MET cc_start: 0.0733 (OUTLIER) cc_final: 0.0001 (ttp) REVERT: D 506 VAL cc_start: 0.3556 (OUTLIER) cc_final: 0.3179 (p) outliers start: 138 outliers final: 86 residues processed: 306 average time/residue: 0.3687 time to fit residues: 190.8533 Evaluate side-chains 263 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 168 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 21 optimal weight: 5.9990 chunk 332 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 76 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 359 optimal weight: 40.0000 chunk 163 optimal weight: 10.0000 chunk 203 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 314 ASN A 331 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 923 GLN A1105 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B 748 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN C 641 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.102733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069566 restraints weight = 148215.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068368 restraints weight = 105574.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068574 restraints weight = 79098.628| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 30584 Z= 0.287 Angle : 0.764 11.500 41640 Z= 0.395 Chirality : 0.047 0.263 4633 Planarity : 0.006 0.068 5380 Dihedral : 5.272 29.559 4060 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.71 % Favored : 91.18 % Rotamer: Outliers : 5.76 % Allowed : 30.74 % Favored : 63.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.84 (0.13), residues: 3742 helix: 0.77 (0.16), residues: 1000 sheet: -1.50 (0.20), residues: 588 loop : -2.23 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 461 HIS 0.008 0.001 HIS C 336 PHE 0.072 0.003 PHE D 40 TYR 0.030 0.002 TYR C 262 ARG 0.008 0.001 ARG C1011 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1019) hydrogen bonds : angle 5.35287 ( 2931) SS BOND : bond 0.01154 ( 40) SS BOND : angle 1.65661 ( 80) covalent geometry : bond 0.00640 (30544) covalent geometry : angle 0.76113 (41560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 156 time to evaluate : 3.706 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: A 51 LEU cc_start: 0.8637 (mm) cc_final: 0.7906 (tp) REVERT: A 132 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7503 (t80) REVERT: A 161 ASN cc_start: 0.9042 (m-40) cc_final: 0.8755 (t0) REVERT: A 174 MET cc_start: 0.1190 (tpt) cc_final: 0.0987 (tpp) REVERT: A 220 LEU cc_start: 0.7627 (tp) cc_final: 0.7074 (tp) REVERT: A 389 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: A 735 CYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7107 (p) REVERT: B 198 PHE cc_start: 0.8288 (m-80) cc_final: 0.7534 (m-80) REVERT: B 201 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: B 290 LEU cc_start: 0.8491 (tt) cc_final: 0.7761 (mt) REVERT: B 477 CYS cc_start: 0.1109 (OUTLIER) cc_final: -0.1775 (p) REVERT: B 792 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7783 (mmtm) REVERT: B 952 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8386 (t0) REVERT: C 81 LEU cc_start: 0.8429 (tt) cc_final: 0.7699 (mm) REVERT: C 101 TRP cc_start: 0.5026 (m-10) cc_final: 0.4149 (m-90) REVERT: C 114 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5578 (tt) REVERT: C 156 VAL cc_start: 0.4972 (OUTLIER) cc_final: 0.4613 (p) REVERT: C 339 PHE cc_start: 0.3678 (OUTLIER) cc_final: 0.2866 (t80) REVERT: C 694 MET cc_start: 0.8957 (mmm) cc_final: 0.8635 (tpt) REVERT: C 1038 ASP cc_start: 0.7195 (t0) cc_final: 0.6950 (t0) REVERT: C 1044 TYR cc_start: 0.8979 (m-80) cc_final: 0.8684 (m-80) REVERT: C 1072 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: D 82 MET cc_start: 0.4542 (ppp) cc_final: 0.4247 (ppp) REVERT: D 192 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7975 (tpm170) REVERT: D 295 ASP cc_start: 0.8708 (t0) cc_final: 0.8279 (p0) REVERT: D 332 MET cc_start: -0.1655 (tmm) cc_final: -0.2474 (ptm) REVERT: D 341 LYS cc_start: 0.9303 (mtmm) cc_final: 0.8994 (tptm) REVERT: D 343 VAL cc_start: 0.6039 (m) cc_final: 0.5678 (p) REVERT: D 427 ASP cc_start: 0.5779 (OUTLIER) cc_final: 0.5504 (m-30) REVERT: D 480 MET cc_start: 0.0761 (OUTLIER) cc_final: 0.0224 (ttp) REVERT: D 506 VAL cc_start: 0.3751 (OUTLIER) cc_final: 0.3367 (p) REVERT: D 578 ASN cc_start: 0.6747 (t0) cc_final: 0.6522 (t0) outliers start: 191 outliers final: 109 residues processed: 332 average time/residue: 0.3601 time to fit residues: 202.0776 Evaluate side-chains 270 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 147 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 951 HIS Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1072 PHE Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 56 optimal weight: 2.9990 chunk 337 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 351 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 369 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 471 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN A 975 ASN A1033 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN B 706 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.101992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.072243 restraints weight = 147518.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071044 restraints weight = 94256.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071650 restraints weight = 70791.065| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 30584 Z= 0.153 Angle : 0.625 9.843 41640 Z= 0.316 Chirality : 0.043 0.180 4633 Planarity : 0.004 0.059 5380 Dihedral : 4.837 28.389 4060 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 4.01 % Allowed : 31.92 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3742 helix: 1.06 (0.17), residues: 992 sheet: -1.40 (0.21), residues: 572 loop : -2.10 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 461 HIS 0.009 0.001 HIS C 336 PHE 0.022 0.002 PHE A 426 TYR 0.020 0.001 TYR A 142 ARG 0.009 0.001 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 1019) hydrogen bonds : angle 4.97663 ( 2931) SS BOND : bond 0.00553 ( 40) SS BOND : angle 1.32857 ( 80) covalent geometry : bond 0.00346 (30544) covalent geometry : angle 0.62264 (41560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 160 time to evaluate : 3.251 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: A 51 LEU cc_start: 0.8451 (mm) cc_final: 0.7716 (tp) REVERT: A 161 ASN cc_start: 0.8930 (m-40) cc_final: 0.8666 (t0) REVERT: A 389 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6227 (m-80) REVERT: A 735 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7103 (p) REVERT: A 866 MET cc_start: 0.8672 (mtt) cc_final: 0.8310 (mtt) REVERT: B 150 MET cc_start: 0.6838 (mmp) cc_final: 0.6474 (mmt) REVERT: B 198 PHE cc_start: 0.8177 (m-80) cc_final: 0.7360 (m-80) REVERT: B 201 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.5756 (m-80) REVERT: B 230 ILE cc_start: 0.4774 (OUTLIER) cc_final: 0.4455 (tt) REVERT: B 477 CYS cc_start: 0.0945 (OUTLIER) cc_final: -0.2043 (p) REVERT: B 792 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7760 (mmtm) REVERT: B 975 ASN cc_start: 0.8867 (m-40) cc_final: 0.8141 (t0) REVERT: B 976 ASP cc_start: 0.8335 (p0) cc_final: 0.8115 (p0) REVERT: C 81 LEU cc_start: 0.8365 (tt) cc_final: 0.7595 (mm) REVERT: C 101 TRP cc_start: 0.5515 (m-10) cc_final: 0.4329 (m-90) REVERT: C 339 PHE cc_start: 0.3905 (OUTLIER) cc_final: 0.3217 (t80) REVERT: C 728 MET cc_start: 0.9190 (ppp) cc_final: 0.7880 (ppp) REVERT: C 756 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 893 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9151 (tt) REVERT: C 1038 ASP cc_start: 0.6926 (t0) cc_final: 0.6669 (t0) REVERT: C 1044 TYR cc_start: 0.8874 (m-80) cc_final: 0.8672 (m-80) REVERT: C 1047 MET cc_start: 0.8387 (tpp) cc_final: 0.7965 (mmm) REVERT: D 82 MET cc_start: 0.4328 (ppp) cc_final: 0.4025 (ppp) REVERT: D 192 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7934 (tpm170) REVERT: D 295 ASP cc_start: 0.8687 (t0) cc_final: 0.8266 (p0) REVERT: D 332 MET cc_start: -0.1580 (tmm) cc_final: -0.2409 (ptm) REVERT: D 341 LYS cc_start: 0.9304 (mtmm) cc_final: 0.8961 (tptm) REVERT: D 427 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.5405 (m-30) REVERT: D 455 MET cc_start: -0.1695 (ttm) cc_final: -0.1974 (tmm) REVERT: D 480 MET cc_start: 0.0545 (OUTLIER) cc_final: -0.0128 (ttp) REVERT: D 506 VAL cc_start: 0.3757 (OUTLIER) cc_final: 0.3422 (p) REVERT: D 557 MET cc_start: 0.1870 (ttt) cc_final: 0.0789 (ttt) REVERT: D 578 ASN cc_start: 0.6684 (t0) cc_final: 0.6391 (t0) outliers start: 133 outliers final: 89 residues processed: 280 average time/residue: 0.3771 time to fit residues: 178.2160 Evaluate side-chains 242 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 141 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 354 optimal weight: 20.0000 chunk 43 optimal weight: 0.0980 chunk 266 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 219 optimal weight: 0.8980 chunk 328 optimal weight: 0.4980 chunk 296 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN A 962 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 951 HIS ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.102907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073842 restraints weight = 148604.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073368 restraints weight = 86860.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.073469 restraints weight = 61671.416| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30584 Z= 0.118 Angle : 0.605 10.467 41640 Z= 0.303 Chirality : 0.043 0.201 4633 Planarity : 0.004 0.061 5380 Dihedral : 4.615 27.556 4060 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 3.29 % Allowed : 32.37 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.14), residues: 3742 helix: 1.20 (0.17), residues: 990 sheet: -1.38 (0.21), residues: 555 loop : -2.01 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 461 HIS 0.008 0.001 HIS C 336 PHE 0.028 0.001 PHE C1072 TYR 0.038 0.001 TYR D 50 ARG 0.009 0.001 ARG C 631 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 1019) hydrogen bonds : angle 4.83164 ( 2931) SS BOND : bond 0.00263 ( 40) SS BOND : angle 1.25277 ( 80) covalent geometry : bond 0.00271 (30544) covalent geometry : angle 0.60313 (41560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 157 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8379 (mm) cc_final: 0.7652 (tp) REVERT: A 132 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7799 (t80) REVERT: A 161 ASN cc_start: 0.8865 (m-40) cc_final: 0.8553 (t0) REVERT: A 389 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: A 494 PHE cc_start: 0.0887 (OUTLIER) cc_final: 0.0144 (m-80) REVERT: A 735 CYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6966 (p) REVERT: A 866 MET cc_start: 0.8540 (mtt) cc_final: 0.8164 (mtt) REVERT: A 987 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: B 150 MET cc_start: 0.6797 (mmp) cc_final: 0.6439 (mmt) REVERT: B 198 PHE cc_start: 0.8043 (m-80) cc_final: 0.7242 (m-80) REVERT: B 230 ILE cc_start: 0.4787 (OUTLIER) cc_final: 0.4497 (tt) REVERT: B 477 CYS cc_start: 0.0656 (OUTLIER) cc_final: -0.2643 (p) REVERT: B 552 SER cc_start: 0.7310 (t) cc_final: 0.6796 (p) REVERT: B 792 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7736 (mmtm) REVERT: B 975 ASN cc_start: 0.8733 (m-40) cc_final: 0.8169 (t0) REVERT: C 81 LEU cc_start: 0.8252 (tt) cc_final: 0.7682 (mm) REVERT: C 101 TRP cc_start: 0.5372 (m-10) cc_final: 0.4309 (m-90) REVERT: C 236 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.6113 (mp-120) REVERT: C 339 PHE cc_start: 0.3655 (OUTLIER) cc_final: 0.3023 (t80) REVERT: C 728 MET cc_start: 0.9081 (ppp) cc_final: 0.7762 (ppp) REVERT: C 1038 ASP cc_start: 0.6608 (t0) cc_final: 0.6316 (t0) REVERT: C 1044 TYR cc_start: 0.8721 (m-80) cc_final: 0.8508 (m-80) REVERT: D 82 MET cc_start: 0.4094 (ppp) cc_final: 0.3804 (ppp) REVERT: D 192 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7870 (tpm170) REVERT: D 295 ASP cc_start: 0.8650 (t0) cc_final: 0.8201 (p0) REVERT: D 332 MET cc_start: -0.1399 (tmm) cc_final: -0.2365 (ptm) REVERT: D 427 ASP cc_start: 0.5639 (OUTLIER) cc_final: 0.5289 (m-30) REVERT: D 480 MET cc_start: 0.0240 (OUTLIER) cc_final: -0.0519 (ttp) REVERT: D 506 VAL cc_start: 0.3493 (OUTLIER) cc_final: 0.3154 (p) REVERT: D 557 MET cc_start: 0.2003 (ttt) cc_final: 0.0838 (ttt) REVERT: D 578 ASN cc_start: 0.6674 (t0) cc_final: 0.6309 (t0) outliers start: 109 outliers final: 80 residues processed: 249 average time/residue: 0.3610 time to fit residues: 152.6100 Evaluate side-chains 238 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 145 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 345 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 170 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.102540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073787 restraints weight = 148341.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.072671 restraints weight = 99476.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073347 restraints weight = 74319.763| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30584 Z= 0.127 Angle : 0.601 10.213 41640 Z= 0.301 Chirality : 0.043 0.211 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.546 27.394 4060 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 3.47 % Allowed : 31.73 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.14), residues: 3742 helix: 1.17 (0.17), residues: 996 sheet: -1.40 (0.21), residues: 553 loop : -1.97 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 461 HIS 0.030 0.001 HIS B 951 PHE 0.029 0.001 PHE B 426 TYR 0.031 0.001 TYR D 50 ARG 0.007 0.000 ARG C 631 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 1019) hydrogen bonds : angle 4.76504 ( 2931) SS BOND : bond 0.00261 ( 40) SS BOND : angle 1.15069 ( 80) covalent geometry : bond 0.00292 (30544) covalent geometry : angle 0.59981 (41560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 154 time to evaluate : 3.217 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: A 132 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 161 ASN cc_start: 0.8923 (m-40) cc_final: 0.8633 (t0) REVERT: A 389 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: A 494 PHE cc_start: 0.1005 (OUTLIER) cc_final: 0.0256 (m-80) REVERT: A 735 CYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6991 (p) REVERT: A 866 MET cc_start: 0.8635 (mtt) cc_final: 0.8241 (mtt) REVERT: A 987 GLU cc_start: 0.8877 (mp0) cc_final: 0.8607 (mp0) REVERT: B 150 MET cc_start: 0.6940 (mmp) cc_final: 0.6640 (mmt) REVERT: B 198 PHE cc_start: 0.8134 (m-80) cc_final: 0.7874 (m-80) REVERT: B 201 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: B 477 CYS cc_start: 0.1060 (OUTLIER) cc_final: -0.1996 (p) REVERT: B 552 SER cc_start: 0.7406 (t) cc_final: 0.6941 (p) REVERT: B 792 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7733 (mmtm) REVERT: B 975 ASN cc_start: 0.8868 (m-40) cc_final: 0.8280 (t0) REVERT: C 81 LEU cc_start: 0.8458 (tt) cc_final: 0.7734 (mm) REVERT: C 101 TRP cc_start: 0.5603 (m-10) cc_final: 0.4426 (m-90) REVERT: C 156 VAL cc_start: 0.5207 (OUTLIER) cc_final: 0.4966 (p) REVERT: C 339 PHE cc_start: 0.3820 (OUTLIER) cc_final: 0.3343 (t80) REVERT: C 694 MET cc_start: 0.9053 (mmm) cc_final: 0.8606 (tpt) REVERT: C 728 MET cc_start: 0.9118 (ppp) cc_final: 0.7756 (ppp) REVERT: C 1038 ASP cc_start: 0.6742 (t0) cc_final: 0.6441 (t0) REVERT: C 1044 TYR cc_start: 0.8785 (m-80) cc_final: 0.8582 (m-80) REVERT: D 82 MET cc_start: 0.4186 (ppp) cc_final: 0.3909 (ppp) REVERT: D 192 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7908 (tpm170) REVERT: D 295 ASP cc_start: 0.8684 (t0) cc_final: 0.8274 (p0) REVERT: D 332 MET cc_start: -0.1481 (tmm) cc_final: -0.2375 (ptm) REVERT: D 427 ASP cc_start: 0.5703 (OUTLIER) cc_final: 0.5378 (m-30) REVERT: D 480 MET cc_start: 0.0312 (ppp) cc_final: -0.0069 (ttp) REVERT: D 506 VAL cc_start: 0.3592 (OUTLIER) cc_final: 0.3262 (p) REVERT: D 557 MET cc_start: 0.2097 (ttt) cc_final: 0.1017 (ttt) REVERT: D 578 ASN cc_start: 0.6633 (t0) cc_final: 0.6296 (t0) outliers start: 115 outliers final: 87 residues processed: 257 average time/residue: 0.3582 time to fit residues: 155.3679 Evaluate side-chains 244 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 146 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 348 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 157 optimal weight: 0.0040 chunk 357 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS ** C 898 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 = 0.4170 r_free = 0.4170 target = 0.102729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.073113 restraints weight = 150539.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.073542 restraints weight = 92101.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.073417 restraints weight = 62908.530| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30584 Z= 0.116 Angle : 0.597 14.318 41640 Z= 0.296 Chirality : 0.043 0.213 4633 Planarity : 0.004 0.061 5380 Dihedral : 4.438 27.094 4060 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 2.93 % Allowed : 32.43 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.14), residues: 3742 helix: 1.21 (0.17), residues: 998 sheet: -1.39 (0.21), residues: 561 loop : -1.92 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 461 HIS 0.009 0.001 HIS B 951 PHE 0.022 0.001 PHE C1072 TYR 0.031 0.001 TYR D 50 ARG 0.007 0.001 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.02863 ( 1019) hydrogen bonds : angle 4.69047 ( 2931) SS BOND : bond 0.00301 ( 40) SS BOND : angle 1.08736 ( 80) covalent geometry : bond 0.00269 (30544) covalent geometry : angle 0.59557 (41560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 156 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASN cc_start: 0.8960 (m-40) cc_final: 0.8694 (t0) REVERT: A 389 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: A 494 PHE cc_start: 0.1089 (OUTLIER) cc_final: 0.0252 (m-80) REVERT: A 728 MET cc_start: 0.8684 (ppp) cc_final: 0.8418 (ppp) REVERT: A 735 CYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7038 (p) REVERT: A 987 GLU cc_start: 0.8908 (mp0) cc_final: 0.8604 (mp0) REVERT: B 150 MET cc_start: 0.6978 (mmp) cc_final: 0.6705 (mmt) REVERT: B 187 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7914 (mtt180) REVERT: B 198 PHE cc_start: 0.8129 (m-80) cc_final: 0.7885 (m-80) REVERT: B 377 TYR cc_start: 0.8622 (t80) cc_final: 0.8138 (t80) REVERT: B 477 CYS cc_start: 0.1291 (OUTLIER) cc_final: -0.1603 (p) REVERT: B 552 SER cc_start: 0.7415 (t) cc_final: 0.7001 (p) REVERT: B 792 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7733 (mmtm) REVERT: B 975 ASN cc_start: 0.8851 (m-40) cc_final: 0.8252 (t0) REVERT: C 81 LEU cc_start: 0.8571 (tt) cc_final: 0.7806 (mm) REVERT: C 101 TRP cc_start: 0.5663 (m-10) cc_final: 0.4476 (m-90) REVERT: C 694 MET cc_start: 0.8996 (mmm) cc_final: 0.8689 (tpt) REVERT: C 728 MET cc_start: 0.9079 (ppp) cc_final: 0.7563 (ppp) REVERT: C 1038 ASP cc_start: 0.6866 (t0) cc_final: 0.6543 (t0) REVERT: C 1044 TYR cc_start: 0.8924 (m-80) cc_final: 0.8670 (m-80) REVERT: D 82 MET cc_start: 0.4334 (ppp) cc_final: 0.4058 (ppp) REVERT: D 192 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7921 (tpm170) REVERT: D 295 ASP cc_start: 0.8682 (t0) cc_final: 0.8286 (p0) REVERT: D 332 MET cc_start: -0.1530 (tmm) cc_final: -0.2385 (ptm) REVERT: D 480 MET cc_start: 0.0472 (ppp) cc_final: -0.0140 (ttp) REVERT: D 506 VAL cc_start: 0.3753 (OUTLIER) cc_final: 0.3418 (p) REVERT: D 557 MET cc_start: 0.2144 (ttt) cc_final: 0.1118 (ttt) REVERT: D 578 ASN cc_start: 0.6606 (t0) cc_final: 0.6268 (t0) outliers start: 97 outliers final: 83 residues processed: 240 average time/residue: 0.3824 time to fit residues: 154.3159 Evaluate side-chains 241 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 152 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 792 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 49 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 155 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.100943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069930 restraints weight = 147673.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.070281 restraints weight = 89492.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070792 restraints weight = 57267.576| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30584 Z= 0.180 Angle : 0.621 10.242 41640 Z= 0.312 Chirality : 0.043 0.210 4633 Planarity : 0.005 0.079 5380 Dihedral : 4.533 27.905 4060 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.52 % Rotamer: Outliers : 2.99 % Allowed : 32.10 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.14), residues: 3742 helix: 1.21 (0.17), residues: 998 sheet: -1.47 (0.20), residues: 574 loop : -1.93 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 461 HIS 0.035 0.001 HIS B 951 PHE 0.020 0.001 PHE C1072 TYR 0.031 0.001 TYR D 50 ARG 0.013 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 1019) hydrogen bonds : angle 4.76605 ( 2931) SS BOND : bond 0.00289 ( 40) SS BOND : angle 1.12583 ( 80) covalent geometry : bond 0.00410 (30544) covalent geometry : angle 0.61916 (41560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10116.97 seconds wall clock time: 178 minutes 24.59 seconds (10704.59 seconds total)