Starting phenix.real_space_refine on Mon Oct 13 03:57:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtj_37835/10_2025/8wtj_37835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtj_37835/10_2025/8wtj_37835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wtj_37835/10_2025/8wtj_37835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtj_37835/10_2025/8wtj_37835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtj_37835/10_2025/8wtj_37835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtj_37835/10_2025/8wtj_37835.map" } resolution = 4.64 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= -0.001 sd= 0.043 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 19139 2.51 5 N 4992 2.21 5 O 5654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29931 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8360 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 4 Chain: "B" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8359 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 4 Chain: "C" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8367 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 4 Chain: "E" 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: 7.26, per 1000 atoms: 0.24 Number of scatterers: 29931 At special positions: 0 Unit cell: (157.04, 165.36, 230.88, 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 5654 8.00 N 4992 7.00 C 19139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.04 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 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 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.04 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7126 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 44 sheets defined 28.9% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.609A pdb=" N GLU A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 733 through 739 removed outlier: 3.746A pdb=" N TYR A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 738 " --> pdb=" O CYS A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.849A pdb=" N SER A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.683A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.621A pdb=" N ALA A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 909 through 937 removed outlier: 3.861A pdb=" N ASN A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 961 removed outlier: 4.214A pdb=" N LEU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.893A pdb=" N ILE A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 4.339A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1028 Processing helix chain 'A' and resid 1112 through 1114 No H-bonds generated for 'chain 'A' and resid 1112 through 1114' Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.948A pdb=" N GLU B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.713A pdb=" N PHE B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 4.079A pdb=" N TRP B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.753A pdb=" N PHE B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 removed outlier: 3.595A pdb=" N VAL B 403 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.949A pdb=" N ILE B 738 " --> pdb=" O CYS B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.608A pdb=" N SER B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 779 removed outlier: 3.860A pdb=" N THR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 801 removed outlier: 4.595A pdb=" N GLN B 800 " --> pdb=" O ASN B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 846 through 852 removed outlier: 3.517A pdb=" N PHE B 851 " --> pdb=" O ALA B 848 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN B 852 " --> pdb=" O GLN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.770A pdb=" N VAL B 911 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 912 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TYR B 913 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 914 " --> pdb=" O VAL B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 908 through 914' Processing helix chain 'B' and resid 915 through 935 removed outlier: 3.838A pdb=" N ALA B 920 " --> pdb=" O GLN B 916 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.752A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 984 removed outlier: 4.059A pdb=" N GLU B 984 " --> pdb=" O ASP B 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 981 through 984' Processing helix chain 'B' and resid 985 through 1028 removed outlier: 4.481A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1114 No H-bonds generated for 'chain 'B' and resid 1112 through 1114' Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.794A pdb=" N GLY C 195 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.427A pdb=" N ILE C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.940A pdb=" N ILE C 406 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.987A pdb=" N SER C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.670A pdb=" N SER C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.732A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 778 " --> pdb=" O THR C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 801 removed outlier: 4.596A pdb=" N GLN C 800 " --> pdb=" O ASN C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 848 through 852 removed outlier: 3.927A pdb=" N PHE C 851 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN C 852 " --> pdb=" O GLN C 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 848 through 852' Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 882 through 887 removed outlier: 3.562A pdb=" N ALA C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 911 through 937 removed outlier: 7.163A pdb=" N LYS C 917 " --> pdb=" O TYR C 913 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 918 " --> pdb=" O GLU C 914 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 937 " --> pdb=" O SER C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 963 removed outlier: 4.473A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 980 Processing helix chain 'C' and resid 981 through 1028 removed outlier: 3.903A pdb=" N GLU C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1114 No H-bonds generated for 'chain 'C' and resid 1112 through 1114' Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.781A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.957A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.742A pdb=" N SER E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 157 through 192 removed outlier: 4.012A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.961A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.737A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.676A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.621A pdb=" N PHE E 327 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.538A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 412 removed outlier: 4.366A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 4.372A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 446 Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 472 through 481 removed outlier: 3.631A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.585A pdb=" N LEU E 503 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 529 removed outlier: 4.164A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.626A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.631A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 588 removed outlier: 3.804A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.609A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.656A pdb=" N ASP A 50 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 269 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.860A pdb=" N GLY A 104 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.043A pdb=" N VAL A 591 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 323 removed outlier: 3.747A pdb=" N LEU A 542 " --> pdb=" O PHE A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 352 removed outlier: 4.159A pdb=" N ASN A 350 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 395 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 394 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 433 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE A 370 " --> pdb=" O ASN A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 550 removed outlier: 4.905A pdb=" N GLU A 579 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 574 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.496A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR A 692 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AB2, first strand: chain 'A' and resid 707 through 711 Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 717 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 717 removed outlier: 6.746A pdb=" N GLY A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER A1051 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1057 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A1059 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A1047 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A1061 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A1043 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 731 Processing sheet with id=AB6, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AB7, first strand: chain 'A' and resid 1090 through 1093 Processing sheet with id=AB8, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.651A pdb=" N SER B 57 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 45 through 48 Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.764A pdb=" N LEU B 81 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B 164 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 220 through 226 removed outlier: 6.692A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 223 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AC5, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.307A pdb=" N GLU B 320 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ASN B 538 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 322 " --> pdb=" O ASN B 538 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 350 through 354 removed outlier: 7.615A pdb=" N ASN B 433 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE B 370 " --> pdb=" O ASN B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 444 through 450 removed outlier: 3.664A pdb=" N GLY B 492 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN B 446 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER B 490 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 448 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU B 488 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 547 through 550 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 656 removed outlier: 4.006A pdb=" N GLU B 650 " --> pdb=" O ILE B 688 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR B 692 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN B 654 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 660 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.587A pdb=" N GLN B1067 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE B 714 " --> pdb=" O PRO B1065 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 716 " --> pdb=" O TYR B1063 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B1063 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 718 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B1061 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR B 720 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B1059 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 722 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B1057 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY B1055 " --> pdb=" O PRO B 724 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B1043 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 730 through 732 Processing sheet with id=AD3, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AD4, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id=AD5, first strand: chain 'C' and resid 25 through 27 removed outlier: 8.366A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE C 199 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AD7, first strand: chain 'C' and resid 49 through 52 Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.559A pdb=" N GLY C 100 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 123 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 168 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AE1, first strand: chain 'C' and resid 320 through 324 removed outlier: 4.219A pdb=" N LEU C 542 " --> pdb=" O PHE C 539 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 392 through 396 removed outlier: 4.069A pdb=" N TRP C 432 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 656 removed outlier: 4.959A pdb=" N THR C 692 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN C 654 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.223A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.223A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1116 through 1117 Processing sheet with id=AE8, first strand: chain 'E' and resid 347 through 350 1094 hydrogen bonds defined for protein. 3045 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: 7.17 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9540 1.34 - 1.46: 7327 1.46 - 1.58: 13611 1.58 - 1.71: 1 1.71 - 1.83: 197 Bond restraints: 30676 Sorted by residual: bond pdb=" CG ARG E 393 " pdb=" CD ARG E 393 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.62e+00 bond pdb=" C ALA B 368 " pdb=" N PRO B 369 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.78e+00 bond pdb=" C ALA A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" CA ARG B 154 " pdb=" CB ARG B 154 " ideal model delta sigma weight residual 1.539 1.626 -0.087 4.88e-02 4.20e+02 3.18e+00 bond pdb=" C ARG E 582 " pdb=" N PRO E 583 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.16e+00 ... (remaining 30671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 41379 3.56 - 7.11: 307 7.11 - 10.67: 44 10.67 - 14.23: 6 14.23 - 17.78: 2 Bond angle restraints: 41738 Sorted by residual: angle pdb=" CB MET E 455 " pdb=" CG MET E 455 " pdb=" SD MET E 455 " ideal model delta sigma weight residual 112.70 130.48 -17.78 3.00e+00 1.11e-01 3.51e+01 angle pdb=" CA MET C 149 " pdb=" CB MET C 149 " pdb=" CG MET C 149 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CB MET C 149 " pdb=" CG MET C 149 " pdb=" SD MET C 149 " ideal model delta sigma weight residual 112.70 127.11 -14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N GLU E 571 " pdb=" CA GLU E 571 " pdb=" CB GLU E 571 " ideal model delta sigma weight residual 110.16 117.05 -6.89 1.48e+00 4.57e-01 2.17e+01 angle pdb=" C GLU E 571 " pdb=" N ASN E 572 " pdb=" CA ASN E 572 " ideal model delta sigma weight residual 121.94 113.04 8.90 2.00e+00 2.50e-01 1.98e+01 ... (remaining 41733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16274 17.93 - 35.86: 1667 35.86 - 53.79: 236 53.79 - 71.71: 69 71.71 - 89.64: 35 Dihedral angle restraints: 18281 sinusoidal: 7204 harmonic: 11077 Sorted by residual: dihedral pdb=" CB CYS A1078 " pdb=" SG CYS A1078 " pdb=" SG CYS A1122 " pdb=" CB CYS A1122 " ideal model delta sinusoidal sigma weight residual -86.00 -169.10 83.10 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 133 " pdb=" CB CYS B 133 " ideal model delta sinusoidal sigma weight residual -86.00 -162.97 76.97 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 133 " pdb=" CB CYS A 133 " ideal model delta sinusoidal sigma weight residual -86.00 -160.91 74.91 1 1.00e+01 1.00e-02 7.10e+01 ... (remaining 18278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3716 0.064 - 0.128: 816 0.128 - 0.192: 97 0.192 - 0.256: 9 0.256 - 0.319: 4 Chirality restraints: 4642 Sorted by residual: chirality pdb=" CB ILE B 98 " pdb=" CA ILE B 98 " pdb=" CG1 ILE B 98 " pdb=" CG2 ILE B 98 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CG LEU A 542 " pdb=" CB LEU A 542 " pdb=" CD1 LEU A 542 " pdb=" CD2 LEU A 542 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE C 199 " pdb=" CA ILE C 199 " pdb=" CG1 ILE C 199 " pdb=" CG2 ILE C 199 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 4639 not shown) Planarity restraints: 5407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 982 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO C 983 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 983 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 983 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 582 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO E 583 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 583 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 583 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 561 " 0.018 2.00e-02 2.50e+03 2.03e-02 7.20e+00 pdb=" CG PHE A 561 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 561 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 561 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 561 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 561 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 561 " -0.002 2.00e-02 2.50e+03 ... (remaining 5404 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5655 2.77 - 3.30: 29732 3.30 - 3.84: 54119 3.84 - 4.37: 60245 4.37 - 4.90: 99061 Nonbonded interactions: 248812 Sorted by model distance: nonbonded pdb=" O THR B 246 " pdb=" OG SER B 250 " model vdw 2.239 3.040 nonbonded pdb=" ND2 ASN E 134 " pdb=" OG SER E 167 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR B 496 " pdb=" OH TYR E 41 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR B 365 " pdb=" O PRO B 380 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP E 382 " pdb=" OH TYR E 385 " model vdw 2.261 3.040 ... (remaining 248807 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 822 or resid 846 through 1136)) selection = (chain 'B' and (resid 14 through 822 or resid 846 through 1136)) selection = (chain 'C' and (resid 14 through 822 or resid 846 through 1136)) } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.140 Find NCS groups from input model: 0.640 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 30717 Z= 0.171 Angle : 0.847 17.783 41820 Z= 0.437 Chirality : 0.052 0.319 4642 Planarity : 0.006 0.086 5407 Dihedral : 14.833 89.642 11032 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.64 % Favored : 91.33 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % 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: -2.46 (0.13), residues: 3761 helix: -0.26 (0.16), residues: 934 sheet: -1.22 (0.21), residues: 586 loop : -2.48 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1010 TYR 0.028 0.002 TYR E 385 PHE 0.045 0.002 PHE A 561 TRP 0.016 0.002 TRP C 432 HIS 0.009 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00347 (30676) covalent geometry : angle 0.84607 (41738) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.19560 ( 82) hydrogen bonds : bond 0.13545 ( 1085) hydrogen bonds : angle 7.11783 ( 3045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9692 (mmp) cc_final: 0.9255 (mmm) REVERT: B 173 MET cc_start: 0.8452 (ppp) cc_final: 0.8242 (ppp) REVERT: B 1099 PHE cc_start: 0.9600 (m-80) cc_final: 0.9119 (m-80) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2006 time to fit residues: 32.9747 Evaluate side-chains 79 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS A 637 ASN A 640 GLN A 770 GLN A 931 GLN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 637 ASN B 903 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 GLN ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1044 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN C 747 ASN C 945 GLN E 34 HIS E 228 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.050010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.026866 restraints weight = 284838.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.027055 restraints weight = 228411.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.027196 restraints weight = 196757.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.027198 restraints weight = 176587.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.027198 restraints weight = 176313.021| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 30717 Z= 0.278 Angle : 0.718 10.439 41820 Z= 0.388 Chirality : 0.044 0.158 4642 Planarity : 0.005 0.068 5407 Dihedral : 5.766 33.001 4077 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.55 % Favored : 90.43 % Rotamer: Outliers : 0.09 % Allowed : 9.10 % Favored : 90.81 % 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: -2.27 (0.13), residues: 3761 helix: 0.11 (0.16), residues: 990 sheet: -1.49 (0.21), residues: 594 loop : -2.40 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 393 TYR 0.023 0.002 TYR E 385 PHE 0.021 0.002 PHE B1105 TRP 0.018 0.002 TRP B1098 HIS 0.012 0.002 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00548 (30676) covalent geometry : angle 0.71744 (41738) SS BOND : bond 0.00405 ( 41) SS BOND : angle 1.13396 ( 82) hydrogen bonds : bond 0.04693 ( 1085) hydrogen bonds : angle 6.22711 ( 3045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9661 (mmp) cc_final: 0.9319 (mmm) REVERT: B 173 MET cc_start: 0.8829 (ppp) cc_final: 0.8419 (ppp) REVERT: B 727 MET cc_start: 0.9597 (pmm) cc_final: 0.9202 (pmm) REVERT: C 578 LEU cc_start: 0.9635 (tp) cc_final: 0.9387 (pt) REVERT: C 727 MET cc_start: 0.8777 (ppp) cc_final: 0.8386 (ppp) outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 0.1945 time to fit residues: 30.2859 Evaluate side-chains 73 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 334 optimal weight: 20.0000 chunk 330 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 249 optimal weight: 7.9990 chunk 309 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 360 optimal weight: 30.0000 chunk 275 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 637 ASN A 640 GLN A 770 GLN ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.049522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.026933 restraints weight = 269920.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.027177 restraints weight = 227008.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.027275 restraints weight = 193677.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027322 restraints weight = 182994.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.027406 restraints weight = 175907.744| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 30717 Z= 0.276 Angle : 0.735 12.379 41820 Z= 0.394 Chirality : 0.046 0.194 4642 Planarity : 0.005 0.064 5407 Dihedral : 5.960 35.115 4077 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.86 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % 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: -2.49 (0.13), residues: 3761 helix: 0.01 (0.16), residues: 993 sheet: -1.64 (0.22), residues: 563 loop : -2.59 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 324 TYR 0.022 0.002 TYR A 608 PHE 0.041 0.003 PHE E 308 TRP 0.016 0.002 TRP B1098 HIS 0.012 0.002 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00552 (30676) covalent geometry : angle 0.73319 (41738) SS BOND : bond 0.00379 ( 41) SS BOND : angle 1.31150 ( 82) hydrogen bonds : bond 0.04701 ( 1085) hydrogen bonds : angle 6.33302 ( 3045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.9078 (ppp) cc_final: 0.8813 (ppp) REVERT: A 898 MET cc_start: 0.9659 (mmp) cc_final: 0.9279 (mmm) REVERT: B 173 MET cc_start: 0.8930 (ppp) cc_final: 0.7788 (ptt) REVERT: C 149 MET cc_start: 0.8180 (pmm) cc_final: 0.7967 (pmm) REVERT: C 727 MET cc_start: 0.8863 (ppp) cc_final: 0.8390 (ppp) REVERT: E 123 MET cc_start: -0.0676 (tmm) cc_final: -0.0999 (tmm) REVERT: E 455 MET cc_start: -0.4802 (pmm) cc_final: -0.5015 (pmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1934 time to fit residues: 28.1948 Evaluate side-chains 68 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 130 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1115 ASN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.050925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032008 restraints weight = 322055.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032293 restraints weight = 246896.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032270 restraints weight = 189166.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.032353 restraints weight = 172208.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.032353 restraints weight = 151491.531| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30717 Z= 0.181 Angle : 0.644 12.075 41820 Z= 0.339 Chirality : 0.044 0.176 4642 Planarity : 0.004 0.063 5407 Dihedral : 5.685 34.523 4077 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.65 % Favored : 90.32 % Rotamer: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % 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: -2.31 (0.13), residues: 3761 helix: 0.32 (0.17), residues: 1005 sheet: -1.48 (0.22), residues: 535 loop : -2.58 (0.12), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 245 TYR 0.018 0.002 TYR A 25 PHE 0.028 0.002 PHE C 894 TRP 0.012 0.001 TRP B1098 HIS 0.010 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00369 (30676) covalent geometry : angle 0.64240 (41738) SS BOND : bond 0.00442 ( 41) SS BOND : angle 1.12580 ( 82) hydrogen bonds : bond 0.04138 ( 1085) hydrogen bonds : angle 5.98744 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.9048 (ppp) cc_final: 0.8795 (ppp) REVERT: A 898 MET cc_start: 0.9651 (mmp) cc_final: 0.9289 (mmm) REVERT: B 173 MET cc_start: 0.8919 (ppp) cc_final: 0.7873 (ptt) REVERT: B 727 MET cc_start: 0.9526 (pmm) cc_final: 0.9159 (pmm) REVERT: C 727 MET cc_start: 0.8742 (ppp) cc_final: 0.8151 (ppp) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1847 time to fit residues: 27.0654 Evaluate side-chains 71 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 353 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 chunk 314 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 164 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN B 560 GLN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 931 GLN ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032649 restraints weight = 338226.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.032923 restraints weight = 249070.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.032763 restraints weight = 187766.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.032763 restraints weight = 161704.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.032763 restraints weight = 161704.799| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30717 Z= 0.157 Angle : 0.622 11.341 41820 Z= 0.326 Chirality : 0.044 0.155 4642 Planarity : 0.004 0.064 5407 Dihedral : 5.533 33.940 4077 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.25 % Favored : 90.72 % Rotamer: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % 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: -2.19 (0.13), residues: 3761 helix: 0.55 (0.17), residues: 987 sheet: -1.50 (0.22), residues: 531 loop : -2.52 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 324 TYR 0.026 0.002 TYR B 497 PHE 0.024 0.002 PHE C 894 TRP 0.014 0.001 TRP E 275 HIS 0.007 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00326 (30676) covalent geometry : angle 0.62004 (41738) SS BOND : bond 0.00321 ( 41) SS BOND : angle 1.35012 ( 82) hydrogen bonds : bond 0.03963 ( 1085) hydrogen bonds : angle 5.81392 ( 3045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9689 (mmp) cc_final: 0.9221 (mmm) REVERT: B 173 MET cc_start: 0.8964 (ppp) cc_final: 0.7949 (ptt) REVERT: B 727 MET cc_start: 0.9482 (pmm) cc_final: 0.9085 (pmm) REVERT: C 727 MET cc_start: 0.8709 (ppp) cc_final: 0.8166 (ppp) REVERT: E 123 MET cc_start: -0.1021 (tmm) cc_final: -0.1345 (tmm) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1825 time to fit residues: 26.6128 Evaluate side-chains 69 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 294 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 355 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.050878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032171 restraints weight = 332461.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032527 restraints weight = 249168.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032527 restraints weight = 183972.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032527 restraints weight = 183967.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032527 restraints weight = 183967.707| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30717 Z= 0.186 Angle : 0.646 11.775 41820 Z= 0.340 Chirality : 0.044 0.172 4642 Planarity : 0.004 0.062 5407 Dihedral : 5.537 34.352 4077 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.97 % Favored : 90.00 % Rotamer: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % 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: -2.20 (0.13), residues: 3761 helix: 0.55 (0.17), residues: 990 sheet: -1.51 (0.22), residues: 542 loop : -2.54 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 324 TYR 0.038 0.002 TYR E 385 PHE 0.024 0.002 PHE A 460 TRP 0.024 0.001 TRP E 203 HIS 0.008 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00379 (30676) covalent geometry : angle 0.64384 (41738) SS BOND : bond 0.00516 ( 41) SS BOND : angle 1.33445 ( 82) hydrogen bonds : bond 0.04026 ( 1085) hydrogen bonds : angle 5.84058 ( 3045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.152 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 727 MET cc_start: 0.9001 (ppp) cc_final: 0.8783 (ppp) REVERT: A 898 MET cc_start: 0.9677 (mmp) cc_final: 0.9272 (mmm) REVERT: B 173 MET cc_start: 0.8993 (ppp) cc_final: 0.7981 (ptt) REVERT: C 578 LEU cc_start: 0.9580 (tp) cc_final: 0.9269 (pt) REVERT: C 727 MET cc_start: 0.8635 (ppp) cc_final: 0.8063 (ppp) REVERT: C 778 PHE cc_start: 0.9136 (m-80) cc_final: 0.8568 (m-80) REVERT: E 123 MET cc_start: -0.0748 (tmm) cc_final: -0.0990 (tmm) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1647 time to fit residues: 23.6281 Evaluate side-chains 70 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 5 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 369 optimal weight: 40.0000 chunk 324 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 chunk 9 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.050731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032153 restraints weight = 332702.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.032488 restraints weight = 250730.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.032668 restraints weight = 181062.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.032439 restraints weight = 174723.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.032439 restraints weight = 151164.003| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30717 Z= 0.191 Angle : 0.655 13.248 41820 Z= 0.343 Chirality : 0.044 0.171 4642 Planarity : 0.004 0.063 5407 Dihedral : 5.548 34.630 4077 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.92 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: -2.22 (0.13), residues: 3761 helix: 0.58 (0.17), residues: 986 sheet: -1.63 (0.22), residues: 553 loop : -2.54 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 245 TYR 0.027 0.002 TYR B 497 PHE 0.021 0.002 PHE C 894 TRP 0.017 0.001 TRP E 203 HIS 0.010 0.002 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00392 (30676) covalent geometry : angle 0.65360 (41738) SS BOND : bond 0.00324 ( 41) SS BOND : angle 1.25870 ( 82) hydrogen bonds : bond 0.04071 ( 1085) hydrogen bonds : angle 5.84571 ( 3045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.183 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 898 MET cc_start: 0.9670 (mmp) cc_final: 0.9413 (mmm) REVERT: B 173 MET cc_start: 0.8863 (ppp) cc_final: 0.7940 (ptt) REVERT: B 727 MET cc_start: 0.9480 (pmm) cc_final: 0.9080 (pmm) REVERT: C 778 PHE cc_start: 0.9156 (m-80) cc_final: 0.8557 (m-80) REVERT: E 297 MET cc_start: 0.0763 (mmp) cc_final: 0.0495 (mmp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1873 time to fit residues: 26.2451 Evaluate side-chains 71 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 358 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 293 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN C 131 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.032745 restraints weight = 337505.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.032994 restraints weight = 256621.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.033124 restraints weight = 192465.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033052 restraints weight = 179878.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033034 restraints weight = 173521.777| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30717 Z= 0.143 Angle : 0.623 11.119 41820 Z= 0.324 Chirality : 0.044 0.162 4642 Planarity : 0.004 0.063 5407 Dihedral : 5.425 34.132 4077 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.73 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -2.09 (0.13), residues: 3761 helix: 0.75 (0.17), residues: 971 sheet: -1.62 (0.22), residues: 552 loop : -2.45 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.023 0.001 TYR B 497 PHE 0.018 0.002 PHE C 52 TRP 0.031 0.001 TRP E 203 HIS 0.008 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00303 (30676) covalent geometry : angle 0.62169 (41738) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.15598 ( 82) hydrogen bonds : bond 0.03837 ( 1085) hydrogen bonds : angle 5.70243 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.9060 (ppp) cc_final: 0.8825 (ppp) REVERT: A 898 MET cc_start: 0.9691 (mmp) cc_final: 0.9434 (mmm) REVERT: B 173 MET cc_start: 0.8905 (ppp) cc_final: 0.7982 (ptt) REVERT: B 727 MET cc_start: 0.9492 (pmm) cc_final: 0.9089 (pmm) REVERT: C 778 PHE cc_start: 0.9234 (m-80) cc_final: 0.8567 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1921 time to fit residues: 27.7805 Evaluate side-chains 72 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 367 optimal weight: 30.0000 chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 344 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 256 optimal weight: 40.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 522 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 = 0.3357 r_free = 0.3357 target = 0.051172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032549 restraints weight = 336490.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.032990 restraints weight = 248784.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033159 restraints weight = 181639.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033178 restraints weight = 155652.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.032930 restraints weight = 144317.394| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30717 Z= 0.148 Angle : 0.627 10.797 41820 Z= 0.325 Chirality : 0.044 0.161 4642 Planarity : 0.004 0.064 5407 Dihedral : 5.378 34.021 4077 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.63 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -2.03 (0.14), residues: 3761 helix: 0.80 (0.17), residues: 973 sheet: -1.46 (0.22), residues: 552 loop : -2.45 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.022 0.001 TYR B 497 PHE 0.017 0.001 PHE E 512 TRP 0.025 0.001 TRP E 203 HIS 0.008 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00312 (30676) covalent geometry : angle 0.62559 (41738) SS BOND : bond 0.00318 ( 41) SS BOND : angle 1.15153 ( 82) hydrogen bonds : bond 0.03818 ( 1085) hydrogen bonds : angle 5.65746 ( 3045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.212 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 898 MET cc_start: 0.9655 (mmp) cc_final: 0.9418 (mmm) REVERT: B 173 MET cc_start: 0.8804 (ppp) cc_final: 0.7964 (ptt) REVERT: B 727 MET cc_start: 0.9467 (pmm) cc_final: 0.9060 (pmm) REVERT: C 727 MET cc_start: 0.8701 (ppp) cc_final: 0.8315 (ppp) REVERT: E 360 MET cc_start: 0.7192 (tmm) cc_final: 0.6952 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1828 time to fit residues: 26.7110 Evaluate side-chains 71 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 348 optimal weight: 0.0670 chunk 196 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 104 optimal weight: 0.0470 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 0.0060 chunk 100 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 23 optimal weight: 30.0000 overall best weight: 1.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN B1094 ASN C 96 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 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 = 0.3446 r_free = 0.3446 target = 0.054976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.037296 restraints weight = 381037.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.036936 restraints weight = 229183.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.037218 restraints weight = 163033.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.037400 restraints weight = 125387.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.037434 restraints weight = 114442.128| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30717 Z= 0.111 Angle : 0.619 14.552 41820 Z= 0.316 Chirality : 0.044 0.203 4642 Planarity : 0.004 0.064 5407 Dihedral : 5.183 33.037 4077 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.93 (0.14), residues: 3761 helix: 0.94 (0.17), residues: 958 sheet: -1.37 (0.22), residues: 567 loop : -2.40 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 462 TYR 0.018 0.001 TYR B 869 PHE 0.019 0.001 PHE E 512 TRP 0.024 0.001 TRP E 203 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00241 (30676) covalent geometry : angle 0.61782 (41738) SS BOND : bond 0.00250 ( 41) SS BOND : angle 1.10934 ( 82) hydrogen bonds : bond 0.03652 ( 1085) hydrogen bonds : angle 5.45914 ( 3045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.255 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 898 MET cc_start: 0.9703 (mmp) cc_final: 0.9384 (mmm) REVERT: B 173 MET cc_start: 0.8633 (ppp) cc_final: 0.8321 (ppp) REVERT: B 727 MET cc_start: 0.9504 (pmm) cc_final: 0.9047 (pmm) REVERT: C 727 MET cc_start: 0.8764 (ppp) cc_final: 0.8389 (ppp) REVERT: C 778 PHE cc_start: 0.9284 (m-80) cc_final: 0.8573 (m-80) REVERT: E 455 MET cc_start: -0.2666 (pmm) cc_final: -0.2967 (pmm) REVERT: E 579 MET cc_start: 0.7569 (tpp) cc_final: 0.7294 (mtm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1806 time to fit residues: 26.1555 Evaluate side-chains 73 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 152 optimal weight: 50.0000 chunk 191 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 165 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 351 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 137 optimal weight: 0.0030 chunk 350 optimal weight: 5.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** E 522 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 = 0.3346 r_free = 0.3346 target = 0.050620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032001 restraints weight = 334569.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032321 restraints weight = 249516.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.032471 restraints weight = 183019.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.032211 restraints weight = 175746.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.032214 restraints weight = 156314.457| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30717 Z= 0.180 Angle : 0.645 11.849 41820 Z= 0.336 Chirality : 0.044 0.177 4642 Planarity : 0.004 0.063 5407 Dihedral : 5.328 33.601 4077 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.76 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -2.00 (0.14), residues: 3761 helix: 0.85 (0.17), residues: 970 sheet: -1.46 (0.22), residues: 542 loop : -2.42 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 324 TYR 0.020 0.002 TYR B 497 PHE 0.016 0.002 PHE E 512 TRP 0.020 0.001 TRP E 203 HIS 0.008 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00370 (30676) covalent geometry : angle 0.64282 (41738) SS BOND : bond 0.00366 ( 41) SS BOND : angle 1.25542 ( 82) hydrogen bonds : bond 0.03902 ( 1085) hydrogen bonds : angle 5.61438 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5945.39 seconds wall clock time: 103 minutes 55.37 seconds (6235.37 seconds total)