Starting phenix.real_space_refine on Mon Aug 25 18:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wro_37784/08_2025/8wro_37784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wro_37784/08_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_37784/08_2025/8wro_37784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wro_37784/08_2025/8wro_37784.map" model { file = "/net/cci-nas-00/data/ceres_data/8wro_37784/08_2025/8wro_37784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wro_37784/08_2025/8wro_37784.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.91, per 1000 atoms: 0.23 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: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.44 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: 7.02 Time building geometry restraints manager: 3.28 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.880 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- 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 : 8.68 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG C1104 TYR 0.024 0.001 TYR C 362 PHE 0.036 0.002 PHE C 397 TRP 0.051 0.002 TRP D 461 HIS 0.009 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00407 (30544) covalent geometry : angle 0.79090 (41560) SS BOND : bond 0.00303 ( 40) SS BOND : angle 1.35246 ( 80) hydrogen bonds : bond 0.14112 ( 1019) hydrogen bonds : angle 6.25269 ( 2931) *********************** 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 : 1.234 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: 0.7817 (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: 0.0997 (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: 0.8524 (mp10) REVERT: A 897 MET cc_start: 0.7268 (tpp) cc_final: 0.6936 (tpp) REVERT: A 987 GLU cc_start: 0.8359 (mp0) cc_final: 0.7896 (mp0) REVERT: B 272 PHE cc_start: 0.7340 (m-80) cc_final: 0.6543 (t80) REVERT: B 570 THR cc_start: 0.8329 (p) cc_final: 0.7774 (t) 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: 0.8043 (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: 0.7903 (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: 0.7102 (mm) REVERT: C 89 PHE cc_start: 0.7108 (t80) cc_final: 0.6511 (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: 0.6322 (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: 0.6503 (m-80) REVERT: C 884 THR cc_start: 0.7886 (p) cc_final: 0.7673 (t) REVERT: D 107 VAL cc_start: 0.7224 (t) cc_final: 0.6835 (t) REVERT: D 295 ASP cc_start: 0.8685 (t0) cc_final: 0.8343 (p0) REVERT: D 577 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8227 (tptt) outliers start: 11 outliers final: 3 residues processed: 472 average time/residue: 0.1868 time to fit residues: 144.3827 Evaluate side-chains 257 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 419 ASN A 954 GLN A1105 ASN B 402 ASN B 474 ASN ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 784 GLN B 853 ASN B 910 GLN B 917 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 131 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 490 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN C 954 GLN C1103 GLN D 61 ASN D 81 GLN D 188 ASN D 429 GLN D 556 ASN D 586 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.113907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.092837 restraints weight = 164795.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.090264 restraints weight = 108910.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.090970 restraints weight = 93530.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.090945 restraints weight = 75766.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.091117 restraints weight = 69595.147| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30584 Z= 0.179 Angle : 0.682 9.838 41640 Z= 0.352 Chirality : 0.045 0.217 4633 Planarity : 0.005 0.077 5380 Dihedral : 4.984 47.430 4067 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Rotamer: Outliers : 4.86 % Allowed : 31.73 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.13), residues: 3742 helix: 0.91 (0.17), residues: 974 sheet: -1.30 (0.21), residues: 589 loop : -2.15 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 495 TYR 0.024 0.002 TYR C 914 PHE 0.027 0.002 PHE B1072 TRP 0.019 0.002 TRP D 461 HIS 0.011 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00402 (30544) covalent geometry : angle 0.67905 (41560) SS BOND : bond 0.00290 ( 40) SS BOND : angle 1.49066 ( 80) hydrogen bonds : bond 0.03785 ( 1019) hydrogen bonds : angle 5.17433 ( 2931) *********************** 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 422 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 261 time to evaluate : 1.128 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: 0.8060 (mm) cc_final: 0.7382 (tp) REVERT: A 126 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7693 (tptt) REVERT: A 321 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: A 402 ASN cc_start: 0.4416 (OUTLIER) cc_final: 0.3536 (p0) REVERT: A 752 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8218 (mp10) REVERT: A 897 MET cc_start: 0.7719 (tpp) cc_final: 0.7470 (tpp) REVERT: A 982 ASP cc_start: 0.7766 (t0) cc_final: 0.7513 (m-30) REVERT: B 98 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5637 (tt) REVERT: B 174 MET cc_start: 0.6158 (ptt) cc_final: 0.5899 (ptp) REVERT: B 187 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6553 (mtt180) REVERT: B 272 PHE cc_start: 0.7201 (m-80) cc_final: 0.6772 (t80) REVERT: B 737 MET cc_start: 0.6968 (tpp) cc_final: 0.6758 (mmm) REVERT: B 744 THR cc_start: 0.8581 (t) cc_final: 0.8247 (t) REVERT: B 748 ASN cc_start: 0.8915 (m-40) cc_final: 0.8548 (m-40) REVERT: B 897 MET cc_start: 0.8538 (tpp) cc_final: 0.8247 (tpp) REVERT: B 1046 LEU cc_start: 0.8508 (mt) cc_final: 0.8215 (tt) REVERT: C 81 LEU cc_start: 0.7637 (tt) cc_final: 0.7078 (mm) REVERT: C 89 PHE cc_start: 0.7527 (t80) cc_final: 0.7137 (t80) REVERT: C 122 ASN cc_start: 0.8142 (m-40) cc_final: 0.7270 (p0) REVERT: C 239 LEU cc_start: 0.7949 (pt) cc_final: 0.7515 (mm) REVERT: C 420 TYR cc_start: 0.6817 (t80) cc_final: 0.6444 (t80) REVERT: C 539 ASN cc_start: 0.7748 (t0) cc_final: 0.6947 (p0) REVERT: C 728 MET cc_start: 0.8905 (ppp) cc_final: 0.7292 (ppp) REVERT: C 982 ASP cc_start: 0.8034 (p0) cc_final: 0.7718 (p0) REVERT: D 74 LYS cc_start: 0.5832 (tptt) cc_final: 0.4982 (tptt) REVERT: D 82 MET cc_start: 0.4083 (ppp) cc_final: 0.3806 (ppp) REVERT: D 295 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8193 (p0) REVERT: D 332 MET cc_start: -0.1133 (tmm) cc_final: -0.2521 (ptp) REVERT: D 427 ASP cc_start: 0.5463 (OUTLIER) cc_final: 0.5179 (m-30) REVERT: D 506 VAL cc_start: 0.3205 (OUTLIER) cc_final: 0.2905 (p) outliers start: 161 outliers final: 62 residues processed: 407 average time/residue: 0.1747 time to fit residues: 118.5081 Evaluate side-chains 278 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 210 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 75 ARG Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 274 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 693 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 791 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1134 VAL 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 392 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 602 SER 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 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 853 ASN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1073 THR 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 396 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 702 VAL 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 958 THR Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 427 ASP 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 365 optimal weight: 40.0000 chunk 67 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 368 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 371 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 361 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 374 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 204 HIS ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS B 853 ASN B 892 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 HIS C 66 HIS C 748 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN C1055 HIS C1122 ASN D 388 GLN D 556 ASN D 580 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.104328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.074618 restraints weight = 153699.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.073821 restraints weight = 100379.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.074601 restraints weight = 76261.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074784 restraints weight = 59239.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074890 restraints weight = 53103.824| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 30584 Z= 0.286 Angle : 0.773 12.561 41640 Z= 0.400 Chirality : 0.047 0.246 4633 Planarity : 0.006 0.065 5380 Dihedral : 5.292 30.155 4060 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.74 % Favored : 91.18 % Rotamer: Outliers : 7.09 % Allowed : 30.68 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.13), residues: 3742 helix: 0.64 (0.16), residues: 999 sheet: -1.47 (0.21), residues: 568 loop : -2.22 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 980 TYR 0.043 0.003 TYR B 348 PHE 0.031 0.002 PHE B 397 TRP 0.044 0.002 TRP C 433 HIS 0.016 0.002 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00638 (30544) covalent geometry : angle 0.77178 (41560) SS BOND : bond 0.00672 ( 40) SS BOND : angle 1.35328 ( 80) hydrogen bonds : bond 0.04273 ( 1019) hydrogen bonds : angle 5.39099 ( 2931) *********************** 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 429 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 194 time to evaluate : 1.254 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 161 ASN cc_start: 0.8994 (m-40) cc_final: 0.8683 (t0) REVERT: A 226 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8088 (tp) REVERT: A 402 ASN cc_start: 0.4309 (OUTLIER) cc_final: 0.3307 (p0) REVERT: A 561 GLN cc_start: 0.8887 (pm20) cc_final: 0.8455 (pp30) REVERT: A 582 LEU cc_start: 0.9442 (pp) cc_final: 0.9173 (mm) REVERT: A 866 MET cc_start: 0.8355 (mtt) cc_final: 0.8074 (mtt) REVERT: B 477 CYS cc_start: 0.1375 (OUTLIER) cc_final: -0.1640 (p) REVERT: B 985 GLU cc_start: 0.8989 (tp30) cc_final: 0.8782 (pt0) REVERT: C 81 LEU cc_start: 0.7981 (tt) cc_final: 0.7541 (mm) REVERT: C 102 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7192 (tp) REVERT: C 114 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.4730 (tt) REVERT: C 175 ASP cc_start: 0.8159 (m-30) cc_final: 0.7907 (p0) REVERT: C 339 PHE cc_start: 0.4554 (OUTLIER) cc_final: 0.4257 (t80) REVERT: C 420 TYR cc_start: 0.7253 (t80) cc_final: 0.6722 (t80) REVERT: C 728 MET cc_start: 0.8919 (ppp) cc_final: 0.7734 (ppp) REVERT: C 1038 ASP cc_start: 0.7071 (t0) cc_final: 0.6817 (t0) REVERT: C 1047 MET cc_start: 0.8016 (mmm) cc_final: 0.7472 (mmm) REVERT: D 60 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6529 (pt0) REVERT: D 190 MET cc_start: 0.2557 (ppp) cc_final: 0.2164 (ppp) REVERT: D 295 ASP cc_start: 0.8713 (t0) cc_final: 0.8248 (p0) REVERT: D 455 MET cc_start: -0.2388 (OUTLIER) cc_final: -0.2856 (tmm) REVERT: D 506 VAL cc_start: 0.3609 (OUTLIER) cc_final: 0.3269 (p) REVERT: D 526 GLN cc_start: 0.7223 (tp40) cc_final: 0.6993 (tm-30) outliers start: 235 outliers final: 118 residues processed: 412 average time/residue: 0.1812 time to fit residues: 125.7669 Evaluate side-chains 294 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 167 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 140 VAL Chi-restraints excluded: chain A residue 226 LEU 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 314 ASN 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 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 693 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 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 948 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL 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 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 607 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 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 852 PHE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain B residue 1119 VAL 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 102 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 238 LEU 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 339 PHE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 584 ILE 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 641 GLN Chi-restraints excluded: chain C residue 702 VAL 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 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 807 SER 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 973 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1006 THR 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 1113 THR Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1134 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 461 TRP 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 366 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 362 optimal weight: 6.9990 chunk 369 optimal weight: 30.0000 chunk 274 optimal weight: 0.6980 chunk 236 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 182 ASN A 314 ASN A 471 GLN A1033 GLN B 182 ASN B 231 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN C 539 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 556 ASN D 580 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.104752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.075524 restraints weight = 151097.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.075612 restraints weight = 93301.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.075595 restraints weight = 65788.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.076049 restraints weight = 61161.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.076231 restraints weight = 48900.243| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30584 Z= 0.151 Angle : 0.615 9.634 41640 Z= 0.313 Chirality : 0.043 0.158 4633 Planarity : 0.005 0.074 5380 Dihedral : 4.866 28.643 4060 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 4.77 % Allowed : 32.28 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.13), residues: 3742 helix: 0.88 (0.16), residues: 1003 sheet: -1.52 (0.21), residues: 572 loop : -2.15 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 518 TYR 0.021 0.001 TYR B 657 PHE 0.022 0.001 PHE B 397 TRP 0.012 0.001 TRP D 477 HIS 0.011 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00340 (30544) covalent geometry : angle 0.61323 (41560) SS BOND : bond 0.00311 ( 40) SS BOND : angle 1.18236 ( 80) hydrogen bonds : bond 0.03291 ( 1019) hydrogen bonds : angle 5.04011 ( 2931) *********************** 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 332 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 174 time to evaluate : 1.190 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 89 PHE cc_start: 0.8827 (t80) cc_final: 0.8430 (t80) REVERT: A 226 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 402 ASN cc_start: 0.4037 (OUTLIER) cc_final: 0.3042 (p0) REVERT: A 582 LEU cc_start: 0.9484 (pp) cc_final: 0.9209 (mm) REVERT: A 735 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6898 (p) REVERT: A 866 MET cc_start: 0.8412 (mtt) cc_final: 0.8088 (mtt) REVERT: A 1129 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 150 MET cc_start: 0.6533 (mmp) cc_final: 0.6310 (mmt) REVERT: B 201 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.5296 (m-80) REVERT: B 477 CYS cc_start: 0.1291 (OUTLIER) cc_final: -0.1714 (p) REVERT: B 584 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7884 (tp) REVERT: C 81 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7629 (mm) REVERT: C 101 TRP cc_start: 0.5326 (m-10) cc_final: 0.4758 (m-90) REVERT: C 339 PHE cc_start: 0.4760 (OUTLIER) cc_final: 0.4514 (t80) REVERT: C 420 TYR cc_start: 0.7479 (t80) cc_final: 0.6590 (t80) REVERT: C 539 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7407 (m-40) REVERT: C 694 MET cc_start: 0.8807 (mmm) cc_final: 0.8436 (tpt) REVERT: C 728 MET cc_start: 0.9098 (ppp) cc_final: 0.7763 (ppp) REVERT: C 756 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 1047 MET cc_start: 0.7604 (mmm) cc_final: 0.6731 (tmm) REVERT: D 74 LYS cc_start: 0.6281 (tptt) cc_final: 0.5350 (tptt) REVERT: D 82 MET cc_start: 0.4761 (ppp) cc_final: 0.4443 (ppp) REVERT: D 192 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8106 (tpm170) REVERT: D 295 ASP cc_start: 0.8718 (t0) cc_final: 0.8286 (p0) REVERT: D 332 MET cc_start: -0.1613 (tmm) cc_final: -0.2435 (ptm) REVERT: D 506 VAL cc_start: 0.3570 (OUTLIER) cc_final: 0.3216 (p) REVERT: D 557 MET cc_start: 0.1722 (tmm) cc_final: 0.1248 (tpt) outliers start: 158 outliers final: 92 residues processed: 319 average time/residue: 0.1865 time to fit residues: 99.4712 Evaluate side-chains 261 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 157 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 75 ARG Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU 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 314 ASN 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 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 689 ILE 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 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 951 HIS 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 1047 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 267 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 548 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1081 ASP 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 139 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 594 VAL 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 702 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 731 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 973 VAL 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 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 506 VAL 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 41 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 370 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 706 ASN B 904 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 HIS D 58 ASN D 556 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.100554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067644 restraints weight = 142229.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069322 restraints weight = 80156.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069489 restraints weight = 46201.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.069992 restraints weight = 36685.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.069966 restraints weight = 34153.049| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 30584 Z= 0.260 Angle : 0.683 9.487 41640 Z= 0.352 Chirality : 0.045 0.178 4633 Planarity : 0.005 0.069 5380 Dihedral : 5.046 29.916 4060 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 6.21 % Allowed : 30.53 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.13), residues: 3742 helix: 0.94 (0.17), residues: 996 sheet: -1.72 (0.20), residues: 584 loop : -2.23 (0.12), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C1011 TYR 0.045 0.002 TYR A 492 PHE 0.029 0.002 PHE C 540 TRP 0.011 0.002 TRP D 461 HIS 0.017 0.002 HIS C 951 Details of bonding type rmsd covalent geometry : bond 0.00579 (30544) covalent geometry : angle 0.68138 (41560) SS BOND : bond 0.00421 ( 40) SS BOND : angle 1.12573 ( 80) hydrogen bonds : bond 0.03475 ( 1019) hydrogen bonds : angle 5.12761 ( 2931) *********************** 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 372 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 166 time to evaluate : 1.268 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 126 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7890 (tptt) REVERT: A 128 CYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5830 (t) REVERT: A 132 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7411 (t80) REVERT: A 389 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 426 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6306 (t80) REVERT: A 582 LEU cc_start: 0.9414 (pp) cc_final: 0.9160 (mm) REVERT: A 735 CYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7176 (p) REVERT: B 98 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.6878 (tt) REVERT: B 176 LEU cc_start: 0.2833 (OUTLIER) cc_final: 0.2503 (mt) REVERT: B 187 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7899 (mtt180) REVERT: B 198 PHE cc_start: 0.8133 (m-80) cc_final: 0.7380 (m-80) REVERT: B 201 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: B 230 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.5055 (tt) REVERT: B 477 CYS cc_start: 0.0993 (OUTLIER) cc_final: -0.2006 (p) REVERT: C 81 LEU cc_start: 0.8238 (tt) cc_final: 0.7461 (mm) REVERT: C 101 TRP cc_start: 0.5540 (m-10) cc_final: 0.4792 (m-90) REVERT: C 339 PHE cc_start: 0.5052 (OUTLIER) cc_final: 0.4495 (t80) REVERT: C 420 TYR cc_start: 0.7847 (t80) cc_final: 0.6683 (t80) REVERT: C 671 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: C 694 MET cc_start: 0.8904 (mmm) cc_final: 0.8613 (tpt) REVERT: C 1044 TYR cc_start: 0.8987 (m-80) cc_final: 0.8706 (m-80) REVERT: C 1047 MET cc_start: 0.8056 (mmm) cc_final: 0.7337 (tmm) REVERT: D 82 MET cc_start: 0.4900 (ppp) cc_final: 0.4562 (ppp) REVERT: D 192 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8210 (tpm170) REVERT: D 295 ASP cc_start: 0.8706 (t0) cc_final: 0.8296 (p0) REVERT: D 332 MET cc_start: -0.1573 (tmm) cc_final: -0.2374 (ptm) REVERT: D 427 ASP cc_start: 0.5688 (OUTLIER) cc_final: 0.5389 (m-30) REVERT: D 476 LYS cc_start: -0.0007 (OUTLIER) cc_final: -0.0295 (tttm) REVERT: D 546 ASN cc_start: 0.3912 (OUTLIER) cc_final: 0.3561 (m-40) outliers start: 206 outliers final: 122 residues processed: 357 average time/residue: 0.1834 time to fit residues: 110.6252 Evaluate side-chains 288 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 151 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 226 LEU 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 426 PHE Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 583 ASP 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 660 ASP Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS 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 805 ASP Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 951 HIS Chi-restraints excluded: chain A residue 960 VAL 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 98 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 176 LEU 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 548 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL 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 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 875 LEU 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 22 THR Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 139 ASP 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 238 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 594 VAL 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 671 TYR 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 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 785 ILE 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 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 973 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1134 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 64 ASN 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 462 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 546 ASN 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 260 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 232 optimal weight: 0.5980 chunk 312 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 279 optimal weight: 8.9990 chunk 288 optimal weight: 0.0270 chunk 276 optimal weight: 3.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 314 ASN A 471 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN B 706 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 641 GLN C 801 GLN C 898 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.102485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070719 restraints weight = 140754.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.072144 restraints weight = 82863.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.072278 restraints weight = 46040.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072428 restraints weight = 43711.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.072528 restraints weight = 39132.415| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30584 Z= 0.118 Angle : 0.599 9.602 41640 Z= 0.303 Chirality : 0.043 0.157 4633 Planarity : 0.004 0.064 5380 Dihedral : 4.721 29.809 4060 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 4.71 % Allowed : 31.95 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.13), residues: 3742 helix: 1.02 (0.17), residues: 1002 sheet: -1.54 (0.21), residues: 576 loop : -2.11 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.058 0.001 TYR D 454 PHE 0.019 0.001 PHE B 397 TRP 0.012 0.001 TRP D 477 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00266 (30544) covalent geometry : angle 0.59657 (41560) SS BOND : bond 0.00236 ( 40) SS BOND : angle 1.25602 ( 80) hydrogen bonds : bond 0.03097 ( 1019) hydrogen bonds : angle 4.81764 ( 2931) *********************** 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 313 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 157 time to evaluate : 1.246 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 389 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: A 426 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5955 (t80) REVERT: A 582 LEU cc_start: 0.9452 (pp) cc_final: 0.9201 (mm) REVERT: A 735 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7065 (p) REVERT: A 1129 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8283 (mm) REVERT: B 98 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7094 (tt) REVERT: B 187 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7665 (ptp-170) REVERT: B 198 PHE cc_start: 0.8111 (m-80) cc_final: 0.7349 (m-80) REVERT: B 201 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5610 (m-80) REVERT: B 230 ILE cc_start: 0.5471 (OUTLIER) cc_final: 0.5180 (tt) REVERT: B 477 CYS cc_start: 0.0754 (OUTLIER) cc_final: -0.2389 (p) REVERT: B 975 ASN cc_start: 0.8700 (m-40) cc_final: 0.8003 (t0) REVERT: B 976 ASP cc_start: 0.7951 (p0) cc_final: 0.7713 (p0) REVERT: C 81 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7668 (mm) REVERT: C 101 TRP cc_start: 0.5656 (m-10) cc_final: 0.4754 (m-90) REVERT: C 339 PHE cc_start: 0.4869 (OUTLIER) cc_final: 0.4348 (t80) REVERT: C 389 PHE cc_start: 0.7816 (m-80) cc_final: 0.7551 (m-10) REVERT: C 395 ASP cc_start: 0.2435 (OUTLIER) cc_final: 0.1941 (t0) REVERT: C 420 TYR cc_start: 0.7799 (t80) cc_final: 0.6987 (t80) REVERT: C 728 MET cc_start: 0.9058 (ppp) cc_final: 0.7829 (ppp) REVERT: C 1038 ASP cc_start: 0.6825 (t0) cc_final: 0.6545 (t0) REVERT: C 1047 MET cc_start: 0.7703 (mmm) cc_final: 0.7108 (tmm) REVERT: D 82 MET cc_start: 0.4555 (ppp) cc_final: 0.4237 (ppp) REVERT: D 192 ARG cc_start: 0.8524 (mtt180) cc_final: 0.8119 (tpm170) REVERT: D 295 ASP cc_start: 0.8677 (t0) cc_final: 0.8259 (p0) REVERT: D 332 MET cc_start: -0.1620 (tmm) cc_final: -0.2449 (ptm) REVERT: D 427 ASP cc_start: 0.5610 (OUTLIER) cc_final: 0.5329 (m-30) REVERT: D 476 LYS cc_start: -0.0333 (OUTLIER) cc_final: -0.0646 (tttm) REVERT: D 578 ASN cc_start: 0.6899 (t0) cc_final: 0.6526 (t0) outliers start: 156 outliers final: 94 residues processed: 300 average time/residue: 0.1792 time to fit residues: 91.5080 Evaluate side-chains 253 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 146 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL 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 426 PHE 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 562 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 702 VAL 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 909 THR Chi-restraints excluded: chain A residue 928 ILE 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 1112 ILE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 ILE 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 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 663 ILE Chi-restraints excluded: chain B residue 702 VAL 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 782 VAL Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 81 LEU 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 238 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 702 VAL 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 785 ILE 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 875 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 973 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 1101 VAL Chi-restraints excluded: chain C residue 1134 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 167 optimal weight: 7.9990 chunk 375 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 331 ASN A 484 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.099575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067249 restraints weight = 140405.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069043 restraints weight = 81230.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068999 restraints weight = 42848.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.069234 restraints weight = 42787.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069202 restraints weight = 40940.951| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30584 Z= 0.225 Angle : 0.660 9.430 41640 Z= 0.336 Chirality : 0.044 0.259 4633 Planarity : 0.005 0.056 5380 Dihedral : 4.866 30.694 4060 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.56 % Rotamer: Outliers : 5.19 % Allowed : 31.58 % Favored : 63.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.13), residues: 3742 helix: 1.02 (0.17), residues: 997 sheet: -1.62 (0.21), residues: 549 loop : -2.16 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 902 TYR 0.042 0.002 TYR C 450 PHE 0.025 0.002 PHE C 640 TRP 0.011 0.001 TRP D 461 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00502 (30544) covalent geometry : angle 0.65897 (41560) SS BOND : bond 0.00347 ( 40) SS BOND : angle 1.16538 ( 80) hydrogen bonds : bond 0.03326 ( 1019) hydrogen bonds : angle 4.97205 ( 2931) *********************** 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 321 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 149 time to evaluate : 1.254 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: A 132 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 174 MET cc_start: 0.1715 (tpp) cc_final: 0.1510 (tpp) REVERT: A 389 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: A 582 LEU cc_start: 0.9454 (pp) cc_final: 0.9205 (mm) REVERT: A 898 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8936 (tt0) REVERT: B 98 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7109 (tt) REVERT: B 187 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7744 (ptp-170) REVERT: B 198 PHE cc_start: 0.8259 (m-80) cc_final: 0.7520 (m-80) REVERT: B 201 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: B 230 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5349 (tt) REVERT: B 272 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: B 290 LEU cc_start: 0.8316 (tt) cc_final: 0.8101 (tp) REVERT: B 477 CYS cc_start: 0.0887 (OUTLIER) cc_final: -0.2142 (p) REVERT: B 975 ASN cc_start: 0.8811 (m-40) cc_final: 0.8089 (t0) REVERT: B 976 ASP cc_start: 0.8115 (p0) cc_final: 0.7879 (p0) REVERT: C 81 LEU cc_start: 0.8363 (tt) cc_final: 0.7608 (mm) REVERT: C 101 TRP cc_start: 0.5982 (m-10) cc_final: 0.4833 (m-90) REVERT: C 287 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6382 (t70) REVERT: C 339 PHE cc_start: 0.4849 (OUTLIER) cc_final: 0.4330 (t80) REVERT: C 420 TYR cc_start: 0.8060 (t80) cc_final: 0.6751 (t80) REVERT: C 694 MET cc_start: 0.8851 (mmm) cc_final: 0.8497 (tpt) REVERT: C 1047 MET cc_start: 0.7850 (mmm) cc_final: 0.7470 (tmm) REVERT: D 82 MET cc_start: 0.4782 (ppp) cc_final: 0.4444 (ppp) REVERT: D 192 ARG cc_start: 0.8502 (mtt180) cc_final: 0.8180 (tpm170) REVERT: D 295 ASP cc_start: 0.8685 (t0) cc_final: 0.8251 (p0) REVERT: D 332 MET cc_start: -0.1425 (tmm) cc_final: -0.2308 (ptm) REVERT: D 476 LYS cc_start: -0.0142 (OUTLIER) cc_final: -0.0594 (tttm) REVERT: D 546 ASN cc_start: 0.4046 (OUTLIER) cc_final: 0.3722 (m-40) REVERT: D 578 ASN cc_start: 0.6999 (t0) cc_final: 0.6622 (t0) outliers start: 172 outliers final: 126 residues processed: 307 average time/residue: 0.1776 time to fit residues: 93.5171 Evaluate side-chains 278 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 140 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 51 LEU 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 132 PHE Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU 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 512 PHE Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 ASP 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 660 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 951 HIS 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 B residue 39 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU 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 272 PHE 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 548 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 702 VAL 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 782 VAL Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 981 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 22 THR Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 139 ASP 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 238 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 594 VAL 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 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 807 SER 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 928 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 973 VAL 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 1101 VAL Chi-restraints excluded: chain D residue 29 LEU 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 462 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 546 ASN 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 82 optimal weight: 2.9990 chunk 229 optimal weight: 0.0770 chunk 44 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 242 HIS ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN B 46 HIS B 484 ASN B 706 ASN B 962 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN C 641 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.100955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069059 restraints weight = 138317.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069734 restraints weight = 82917.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070191 restraints weight = 59403.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070880 restraints weight = 41163.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070760 restraints weight = 33049.803| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.7762 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= 0.121 Angle : 0.602 10.439 41640 Z= 0.302 Chirality : 0.043 0.152 4633 Planarity : 0.005 0.067 5380 Dihedral : 4.637 29.621 4060 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 4.16 % Allowed : 32.73 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.13), residues: 3742 helix: 1.10 (0.17), residues: 996 sheet: -1.56 (0.21), residues: 558 loop : -2.07 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 75 TYR 0.035 0.001 TYR D 454 PHE 0.018 0.001 PHE B 397 TRP 0.032 0.001 TRP D 203 HIS 0.010 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00274 (30544) covalent geometry : angle 0.60055 (41560) SS BOND : bond 0.00282 ( 40) SS BOND : angle 1.13365 ( 80) hydrogen bonds : bond 0.03067 ( 1019) hydrogen bonds : angle 4.74793 ( 2931) *********************** 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 292 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 154 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7946 (tptt) REVERT: A 132 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 389 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: A 426 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5936 (t80) REVERT: A 494 PHE cc_start: 0.1780 (OUTLIER) cc_final: 0.0843 (m-80) REVERT: A 582 LEU cc_start: 0.9443 (pp) cc_final: 0.9208 (mm) REVERT: A 735 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7052 (p) REVERT: A 982 ASP cc_start: 0.8666 (t0) cc_final: 0.8360 (m-30) REVERT: B 150 MET cc_start: 0.7151 (mmp) cc_final: 0.6873 (mmt) REVERT: B 198 PHE cc_start: 0.8194 (m-80) cc_final: 0.7447 (m-80) REVERT: B 201 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: B 230 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5455 (tt) REVERT: B 272 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: B 477 CYS cc_start: 0.1019 (OUTLIER) cc_final: -0.1904 (p) REVERT: B 552 SER cc_start: 0.7505 (t) cc_final: 0.6970 (p) REVERT: B 975 ASN cc_start: 0.8669 (m-40) cc_final: 0.8101 (t0) REVERT: C 81 LEU cc_start: 0.8348 (tt) cc_final: 0.7698 (mm) REVERT: C 101 TRP cc_start: 0.5671 (m-10) cc_final: 0.4649 (m-90) REVERT: C 339 PHE cc_start: 0.4764 (OUTLIER) cc_final: 0.4155 (t80) REVERT: C 395 ASP cc_start: 0.2645 (OUTLIER) cc_final: 0.2088 (t0) REVERT: C 420 TYR cc_start: 0.8118 (t80) cc_final: 0.7180 (t80) REVERT: C 728 MET cc_start: 0.9066 (ppp) cc_final: 0.8510 (ppp) REVERT: C 1038 ASP cc_start: 0.7019 (t0) cc_final: 0.6697 (t0) REVERT: D 82 MET cc_start: 0.4695 (ppp) cc_final: 0.4385 (ppp) REVERT: D 192 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8176 (tpm170) REVERT: D 295 ASP cc_start: 0.8681 (t0) cc_final: 0.8280 (p0) REVERT: D 332 MET cc_start: -0.1608 (tmm) cc_final: -0.2321 (ptm) REVERT: D 578 ASN cc_start: 0.6978 (t0) cc_final: 0.6584 (t0) outliers start: 138 outliers final: 103 residues processed: 282 average time/residue: 0.1849 time to fit residues: 88.0122 Evaluate side-chains 261 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 147 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 51 LEU 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 137 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL 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 426 PHE 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 562 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 566 ILE 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 660 ASP Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU 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 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU 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 271 THR Chi-restraints excluded: chain B residue 272 PHE 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 594 VAL 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 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL 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 B residue 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 584 ILE 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 731 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 785 ILE 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 928 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 973 VAL 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 1101 VAL 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 462 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 315 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 352 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.100366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068572 restraints weight = 139348.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069573 restraints weight = 84073.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069805 restraints weight = 52960.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.070119 restraints weight = 42547.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070170 restraints weight = 39373.565| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.7964 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= 0.149 Angle : 0.609 10.742 41640 Z= 0.306 Chirality : 0.043 0.176 4633 Planarity : 0.004 0.058 5380 Dihedral : 4.602 29.714 4060 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.60 % Rotamer: Outliers : 3.92 % Allowed : 32.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.13), residues: 3742 helix: 1.11 (0.17), residues: 1007 sheet: -1.49 (0.21), residues: 546 loop : -2.05 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 582 TYR 0.023 0.001 TYR C 450 PHE 0.033 0.001 PHE B 426 TRP 0.017 0.001 TRP D 477 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00338 (30544) covalent geometry : angle 0.60714 (41560) SS BOND : bond 0.00309 ( 40) SS BOND : angle 1.11994 ( 80) hydrogen bonds : bond 0.03026 ( 1019) hydrogen bonds : angle 4.74706 ( 2931) *********************** 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 275 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 145 time to evaluate : 1.173 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: A 126 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7973 (tptt) REVERT: A 389 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 426 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.6032 (t80) REVERT: A 494 PHE cc_start: 0.1404 (OUTLIER) cc_final: 0.0601 (m-80) REVERT: A 582 LEU cc_start: 0.9452 (pp) cc_final: 0.9200 (mm) REVERT: A 735 CYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6999 (p) REVERT: B 150 MET cc_start: 0.7170 (mmp) cc_final: 0.6753 (mmt) REVERT: B 198 PHE cc_start: 0.8235 (m-80) cc_final: 0.7490 (m-80) REVERT: B 201 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: B 230 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5602 (tt) REVERT: B 272 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: B 477 CYS cc_start: 0.1019 (OUTLIER) cc_final: -0.1916 (p) REVERT: B 975 ASN cc_start: 0.8801 (m-40) cc_final: 0.8241 (t0) REVERT: C 81 LEU cc_start: 0.8430 (tt) cc_final: 0.7662 (mm) REVERT: C 101 TRP cc_start: 0.5934 (m-10) cc_final: 0.4780 (m-90) REVERT: C 339 PHE cc_start: 0.4622 (OUTLIER) cc_final: 0.3931 (t80) REVERT: C 395 ASP cc_start: 0.2966 (OUTLIER) cc_final: 0.2352 (t0) REVERT: C 420 TYR cc_start: 0.8132 (t80) cc_final: 0.7203 (t80) REVERT: C 1038 ASP cc_start: 0.6785 (t0) cc_final: 0.6490 (t0) REVERT: D 82 MET cc_start: 0.4714 (ppp) cc_final: 0.4403 (ppp) REVERT: D 192 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8205 (tpm170) REVERT: D 295 ASP cc_start: 0.8679 (t0) cc_final: 0.8268 (p0) REVERT: D 332 MET cc_start: -0.1443 (tmm) cc_final: -0.2228 (ptm) REVERT: D 506 VAL cc_start: 0.3715 (OUTLIER) cc_final: 0.3397 (p) REVERT: D 523 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6205 (t80) REVERT: D 578 ASN cc_start: 0.7149 (t0) cc_final: 0.6765 (t0) outliers start: 130 outliers final: 105 residues processed: 268 average time/residue: 0.1770 time to fit residues: 81.2742 Evaluate side-chains 259 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 142 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 51 LEU 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 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL 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 426 PHE 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 562 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 566 ILE 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 660 ASP Chi-restraints excluded: chain A residue 702 VAL 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 909 THR Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU 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 272 PHE 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 585 THR Chi-restraints excluded: chain B residue 594 VAL 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 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL 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 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 498 TYR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 584 ILE 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 671 TYR 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 785 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 807 SER 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 928 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 973 VAL 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 1101 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 176 LEU 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 462 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 531 GLN 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 244 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 784 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 641 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN D 340 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.099146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067119 restraints weight = 138251.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067863 restraints weight = 83547.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068461 restraints weight = 53796.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.068800 restraints weight = 38815.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068828 restraints weight = 35245.213| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.8354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 30584 Z= 0.194 Angle : 0.648 15.819 41640 Z= 0.327 Chirality : 0.043 0.189 4633 Planarity : 0.004 0.056 5380 Dihedral : 4.722 29.993 4060 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.96 % Rotamer: Outliers : 3.77 % Allowed : 32.88 % Favored : 63.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 3742 helix: 1.13 (0.17), residues: 996 sheet: -1.49 (0.21), residues: 543 loop : -2.08 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 187 TYR 0.023 0.002 TYR C 450 PHE 0.021 0.001 PHE B 426 TRP 0.016 0.001 TRP B 101 HIS 0.011 0.001 HIS A1080 Details of bonding type rmsd covalent geometry : bond 0.00437 (30544) covalent geometry : angle 0.64662 (41560) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.16848 ( 80) hydrogen bonds : bond 0.03115 ( 1019) hydrogen bonds : angle 4.81676 ( 2931) ********************** 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 276 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 151 time to evaluate : 1.289 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 126 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8054 (tptt) REVERT: A 389 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: A 426 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.6063 (t80) REVERT: A 494 PHE cc_start: 0.1617 (OUTLIER) cc_final: 0.0632 (m-80) REVERT: A 582 LEU cc_start: 0.9442 (pp) cc_final: 0.9203 (mm) REVERT: B 150 MET cc_start: 0.7356 (mmp) cc_final: 0.6995 (mmt) REVERT: B 198 PHE cc_start: 0.8394 (m-80) cc_final: 0.7641 (m-80) REVERT: B 201 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: B 272 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: B 377 TYR cc_start: 0.8430 (t80) cc_final: 0.7982 (t80) REVERT: B 477 CYS cc_start: 0.1182 (OUTLIER) cc_final: -0.1639 (p) REVERT: B 975 ASN cc_start: 0.8777 (m-40) cc_final: 0.8235 (t0) REVERT: C 81 LEU cc_start: 0.8427 (tt) cc_final: 0.7663 (mm) REVERT: C 101 TRP cc_start: 0.6096 (m-10) cc_final: 0.4902 (m-90) REVERT: C 339 PHE cc_start: 0.4760 (OUTLIER) cc_final: 0.4050 (t80) REVERT: C 777 GLU cc_start: 0.8673 (pm20) cc_final: 0.8093 (pp20) REVERT: D 82 MET cc_start: 0.4724 (ppp) cc_final: 0.4410 (ppp) REVERT: D 192 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8244 (tpm170) REVERT: D 295 ASP cc_start: 0.8592 (t0) cc_final: 0.8155 (p0) REVERT: D 332 MET cc_start: -0.1404 (tmm) cc_final: -0.2193 (ptm) REVERT: D 506 VAL cc_start: 0.3669 (OUTLIER) cc_final: 0.3332 (p) REVERT: D 523 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6289 (t80) REVERT: D 578 ASN cc_start: 0.7063 (t0) cc_final: 0.6671 (t0) outliers start: 125 outliers final: 109 residues processed: 269 average time/residue: 0.1792 time to fit residues: 82.2836 Evaluate side-chains 267 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 149 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 51 LEU 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 188 GLU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL 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 426 PHE 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 562 PHE Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 566 ILE 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 660 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 928 ILE 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 B residue 39 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 PHE 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 585 THR Chi-restraints excluded: chain B residue 594 VAL 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 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL 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 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 336 HIS 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 498 TYR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 584 ILE 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 671 TYR 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 785 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 807 SER 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 928 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 973 VAL 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 1101 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 531 GLN 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 253 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 165 optimal weight: 0.3980 chunk 342 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 363 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 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 = 0.4102 r_free = 0.4102 target = 0.100435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.068630 restraints weight = 139899.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069286 restraints weight = 88241.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070163 restraints weight = 55774.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.070570 restraints weight = 40162.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070475 restraints weight = 32873.417| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30584 Z= 0.117 Angle : 0.611 14.290 41640 Z= 0.306 Chirality : 0.043 0.151 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.596 29.212 4060 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.73 % Rotamer: Outliers : 3.50 % Allowed : 33.09 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.13), residues: 3742 helix: 1.21 (0.17), residues: 989 sheet: -1.40 (0.21), residues: 551 loop : -2.03 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 631 TYR 0.023 0.001 TYR B 418 PHE 0.017 0.001 PHE C 640 TRP 0.016 0.001 TRP D 477 HIS 0.008 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00264 (30544) covalent geometry : angle 0.60998 (41560) SS BOND : bond 0.00277 ( 40) SS BOND : angle 1.10617 ( 80) hydrogen bonds : bond 0.02905 ( 1019) hydrogen bonds : angle 4.66893 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6240.28 seconds wall clock time: 108 minutes 55.29 seconds (6535.29 seconds total)