Starting phenix.real_space_refine on Thu Mar 5 21:51:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhl_31998/03_2026/7vhl_31998.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhl_31998/03_2026/7vhl_31998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vhl_31998/03_2026/7vhl_31998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhl_31998/03_2026/7vhl_31998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vhl_31998/03_2026/7vhl_31998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhl_31998/03_2026/7vhl_31998.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 117 5.16 5 C 16252 2.51 5 N 4244 2.21 5 O 4849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25462 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 8526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8526 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 2 Chain: "B" Number of atoms: 8441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8441 Classifications: {'peptide': 1083} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 54, 'TRANS': 1028} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 8495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8495 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 54, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 5.47, per 1000 atoms: 0.21 Number of scatterers: 25462 At special positions: 0 Unit cell: (153.92, 149.76, 197.6, 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 117 16.00 O 4849 8.00 N 4244 7.00 C 16252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 581 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C1016 " - pdb=" SG CYS C1027 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.05 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B1016 " - pdb=" SG CYS B1027 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 744 " distance=2.02 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A1016 " - pdb=" SG CYS A1027 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6106 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 50 sheets defined 24.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.539A pdb=" N ASN C 128 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.644A pdb=" N VAL C 398 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 610 through 615 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 730 through 740 Processing helix chain 'C' and resid 742 through 767 Processing helix chain 'C' and resid 800 through 810 removed outlier: 3.652A pdb=" N VAL C 810 " --> pdb=" O LEU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 850 through 867 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.245A pdb=" N LEU C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 923 removed outlier: 3.804A pdb=" N SER C 923 " --> pdb=" O GLN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 949 Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 968 removed outlier: 3.515A pdb=" N ILE C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 972 Processing helix chain 'C' and resid 973 through 1017 Processing helix chain 'C' and resid 1124 through 1129 removed outlier: 4.174A pdb=" N GLU C1128 " --> pdb=" O PRO C1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.585A pdb=" N TRP B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 375 through 379 removed outlier: 4.019A pdb=" N ASN B 379 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 4.379A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.513A pdb=" N TYR B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 610 through 614 removed outlier: 3.798A pdb=" N VAL B 613 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.568A pdb=" N ASN B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 738 " --> pdb=" O SER B 734 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 739 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.551A pdb=" N GLN B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 753 " --> pdb=" O ARG B 749 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 760 " --> pdb=" O VAL B 756 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 762 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 809 removed outlier: 3.562A pdb=" N LEU B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 Processing helix chain 'B' and resid 850 through 868 Processing helix chain 'B' and resid 870 through 875 removed outlier: 3.912A pdb=" N ALA B 874 " --> pdb=" O TRP B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 891 Processing helix chain 'B' and resid 892 through 894 No H-bonds generated for 'chain 'B' and resid 892 through 894' Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.202A pdb=" N LEU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 901 " --> pdb=" O GLN B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 923 Processing helix chain 'B' and resid 924 through 928 removed outlier: 6.870A pdb=" N SER B 927 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 928 " --> pdb=" O THR B 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 924 through 928' Processing helix chain 'B' and resid 929 through 950 removed outlier: 3.706A pdb=" N GLN B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 968 removed outlier: 3.651A pdb=" N ILE B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1016 removed outlier: 3.841A pdb=" N GLU B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 980 " --> pdb=" O GLN B 976 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 985 " --> pdb=" O ILE B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1125 through 1131 removed outlier: 3.852A pdb=" N ASP B1130 " --> pdb=" O PRO B1127 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER B1131 " --> pdb=" O GLU B1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.774A pdb=" N LEU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.227A pdb=" N ASN A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.607A pdb=" N VAL A 398 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 399' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 742 through 767 removed outlier: 3.738A pdb=" N PHE A 766 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 removed outlier: 3.510A pdb=" N ASP A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 850 through 868 Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.948A pdb=" N ALA A 874 " --> pdb=" O TRP A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.344A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 923 Processing helix chain 'A' and resid 925 through 928 removed outlier: 3.903A pdb=" N ALA A 928 " --> pdb=" O THR A 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 968 removed outlier: 3.568A pdb=" N ILE A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1015 removed outlier: 6.010A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 removed outlier: 3.914A pdb=" N GLU A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.813A pdb=" N THR C 51 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 266 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 66 removed outlier: 4.025A pdb=" N ALA C 255 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 86 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 81 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 180 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 199 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 4.025A pdb=" N ALA C 255 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 86 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 81 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 195 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.207A pdb=" N VAL C 117 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 302 through 304 removed outlier: 3.558A pdb=" N THR C 590 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 316 through 319 removed outlier: 3.702A pdb=" N ARG C 319 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 544 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 565 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY C 557 " --> pdb=" O ASP C 565 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.581A pdb=" N ILE C 349 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 386 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 424 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 369 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN C 428 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 365 " --> pdb=" O ASN C 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 352 through 353 removed outlier: 7.081A pdb=" N CYS C 352 " --> pdb=" O CYS C 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 443 through 445 Processing sheet with id=AB1, first strand: chain 'C' and resid 645 through 646 removed outlier: 5.436A pdb=" N GLU C 645 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR C 680 " --> pdb=" O GLU C 645 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 679 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 685 through 687 Processing sheet with id=AB3, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.574A pdb=" N THR C1060 " --> pdb=" O SER C1081 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 706 removed outlier: 3.680A pdb=" N THR C1050 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET C1034 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR C1051 " --> pdb=" O HIS C1032 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HIS C1032 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 709 through 712 Processing sheet with id=AB6, first strand: chain 'C' and resid 718 through 720 removed outlier: 3.696A pdb=" N THR C 843 " --> pdb=" O SER C 719 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 771 through 774 removed outlier: 5.294A pdb=" N ILE C 772 " --> pdb=" O ASN B 687 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1104 through 1109 removed outlier: 6.079A pdb=" N VAL C1106 " --> pdb=" O PHE C1073 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE C1073 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY C1108 " --> pdb=" O ALA C1071 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 removed outlier: 4.183A pdb=" N THR B 63 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 258 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 255 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 84 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 81 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 194 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 196 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 215 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.614A pdb=" N ASP B 53 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.636A pdb=" N VAL B 111 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 118 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 117 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 163 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 removed outlier: 4.122A pdb=" N ASP B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 302 through 308 removed outlier: 5.446A pdb=" N ILE B 303 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 590 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 305 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 588 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 307 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 589 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 315 through 316 removed outlier: 6.872A pdb=" N GLU B 315 " --> pdb=" O ASN B 531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.669A pdb=" N VAL B 386 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 505 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.777A pdb=" N CYS B 516 " --> pdb=" O CYS B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.624A pdb=" N THR B 367 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 500 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 501 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 391 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 443 through 445 Processing sheet with id=AD1, first strand: chain 'B' and resid 633 through 636 Processing sheet with id=AD2, first strand: chain 'B' and resid 645 through 646 removed outlier: 4.086A pdb=" N SER B 675 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 677 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 679 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 695 through 697 removed outlier: 4.114A pdb=" N THR B1060 " --> pdb=" O SER B1081 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 703 through 712 removed outlier: 3.576A pdb=" N GLY B1043 " --> pdb=" O ALA B1040 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR B1051 " --> pdb=" O HIS B1032 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS B1032 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 771 through 774 removed outlier: 6.034A pdb=" N ILE B 772 " --> pdb=" O ASN A 687 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 5.931A pdb=" N VAL B1106 " --> pdb=" O PHE B1073 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B1073 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B1108 " --> pdb=" O ALA B1071 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 50 through 55 removed outlier: 6.950A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.777A pdb=" N THR A 63 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 258 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.888A pdb=" N GLU A 87 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 199 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 97 through 98 removed outlier: 4.174A pdb=" N GLY A 98 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.813A pdb=" N VAL A 218 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 196 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AE4, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AE5, first strand: chain 'A' and resid 316 through 319 removed outlier: 3.646A pdb=" N VAL A 530 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.829A pdb=" N ILE A 349 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 386 " --> pdb=" O ILE A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.703A pdb=" N CYS A 352 " --> pdb=" O CYS A 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.848A pdb=" N THR A 367 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 426 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 369 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP A 427 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 645 through 646 removed outlier: 5.746A pdb=" N GLU A 645 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR A 680 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 695 through 697 removed outlier: 3.652A pdb=" N THR A1060 " --> pdb=" O SER A1081 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AF3, first strand: chain 'A' and resid 705 through 712 removed outlier: 7.103A pdb=" N GLY A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER A1039 " --> pdb=" O GLY A1043 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A1045 " --> pdb=" O PRO A1037 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A1047 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A1035 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1049 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1065 through 1066 Processing sheet with id=AF5, first strand: chain 'A' and resid 1070 through 1074 removed outlier: 5.593A pdb=" N ALA A1071 " --> pdb=" O SER A1107 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2127 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.38 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: 8239 1.34 - 1.46: 6367 1.46 - 1.59: 11311 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 26064 Sorted by residual: bond pdb=" N CYS B 327 " pdb=" CA CYS B 327 " ideal model delta sigma weight residual 1.458 1.485 -0.028 7.40e-03 1.83e+04 1.40e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.456 1.490 -0.033 9.50e-03 1.11e+04 1.23e+01 bond pdb=" N THR B 324 " pdb=" CA THR B 324 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.52e+00 bond pdb=" N LEU B 326 " pdb=" CA LEU B 326 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.35e+00 bond pdb=" C CYS B 327 " pdb=" N PRO B 328 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.30e-02 5.92e+03 3.23e+00 ... (remaining 26059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 34980 1.88 - 3.75: 442 3.75 - 5.63: 56 5.63 - 7.51: 11 7.51 - 9.38: 3 Bond angle restraints: 35492 Sorted by residual: angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 113.53 104.15 9.38 9.80e-01 1.04e+00 9.16e+01 angle pdb=" O ASN B 325 " pdb=" C ASN B 325 " pdb=" N LEU B 326 " ideal model delta sigma weight residual 122.09 126.44 -4.35 1.04e+00 9.25e-01 1.75e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA CYS B 327 " pdb=" C CYS B 327 " pdb=" O CYS B 327 " ideal model delta sigma weight residual 120.48 117.48 3.00 7.70e-01 1.69e+00 1.51e+01 angle pdb=" C ASP A 605 " pdb=" N VAL A 606 " pdb=" CA VAL A 606 " ideal model delta sigma weight residual 121.97 128.12 -6.15 1.80e+00 3.09e-01 1.17e+01 ... (remaining 35487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13973 17.98 - 35.95: 1309 35.95 - 53.93: 182 53.93 - 71.91: 30 71.91 - 89.88: 33 Dihedral angle restraints: 15527 sinusoidal: 6021 harmonic: 9506 Sorted by residual: dihedral pdb=" CB CYS A 653 " pdb=" SG CYS A 653 " pdb=" SG CYS A 662 " pdb=" CB CYS A 662 " ideal model delta sinusoidal sigma weight residual -86.00 1.53 -87.53 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS B 327 " pdb=" SG CYS B 327 " pdb=" SG CYS B 352 " pdb=" CB CYS B 352 " ideal model delta sinusoidal sigma weight residual -86.00 -7.79 -78.21 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS C1066 " pdb=" SG CYS C1066 " pdb=" SG CYS C1110 " pdb=" CB CYS C1110 " ideal model delta sinusoidal sigma weight residual 93.00 35.78 57.22 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 15524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3273 0.051 - 0.102: 613 0.102 - 0.153: 124 0.153 - 0.205: 4 0.205 - 0.256: 3 Chirality restraints: 4017 Sorted by residual: chirality pdb=" CA ILE B 323 " pdb=" N ILE B 323 " pdb=" C ILE B 323 " pdb=" CB ILE B 323 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL A 606 " pdb=" CA VAL A 606 " pdb=" CG1 VAL A 606 " pdb=" CG2 VAL A 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASN B 325 " pdb=" N ASN B 325 " pdb=" C ASN B 325 " pdb=" CB ASN B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 4014 not shown) Planarity restraints: 4613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 469 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO C 470 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 322 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C ASN B 322 " -0.067 2.00e-02 2.50e+03 pdb=" O ASN B 322 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE B 323 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 775 " -0.036 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO C 776 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 776 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 776 " -0.031 5.00e-02 4.00e+02 ... (remaining 4610 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 915 2.71 - 3.26: 26667 3.26 - 3.80: 41092 3.80 - 4.35: 50903 4.35 - 4.90: 84741 Nonbonded interactions: 204318 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 265 " model vdw 2.161 3.040 nonbonded pdb=" O ASP C 411 " pdb=" NH2 ARG C 448 " model vdw 2.187 3.120 nonbonded pdb=" OG SER A 340 " pdb=" O LEU A 443 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" O LYS C 178 " model vdw 2.193 3.040 nonbonded pdb=" O LEU B 950 " pdb=" OG SER B 959 " model vdw 2.207 3.040 ... (remaining 204313 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 345 or (resid 346 and (name N or name CA or nam \ e C or name O or name CB )) or resid 347 through 612 or resid 626 or resid 631 t \ hrough 1131)) selection = (chain 'B' and (resid 14 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 through 613 or resid 631 through 1131)) \ selection = (chain 'C' and (resid 14 through 185 or (resid 186 and (name N or name CA or nam \ e C or name O or name CB )) or resid 187 through 345 or (resid 346 and (name N o \ r name CA or name C or name O or name CB )) or resid 347 through 518 or (resid 5 \ 19 and (name N or name CA or name C or name O or name CB )) or resid 520 through \ 613 or resid 631 through 812 or resid 833 through 1131)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.510 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.002 0.038 26103 Z= 0.116 Angle : 0.545 9.381 35570 Z= 0.292 Chirality : 0.042 0.256 4017 Planarity : 0.004 0.108 4613 Dihedral : 13.845 89.882 9304 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 3245 helix: 1.43 (0.21), residues: 686 sheet: -0.96 (0.22), residues: 584 loop : -1.71 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 889 TYR 0.015 0.001 TYR A 161 PHE 0.017 0.001 PHE B 126 TRP 0.026 0.001 TRP A 143 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00237 (26064) covalent geometry : angle 0.54274 (35492) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.11676 ( 78) hydrogen bonds : bond 0.22117 ( 768) hydrogen bonds : angle 8.86287 ( 2127) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: C 758 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7226 (mm-40) REVERT: B 108 LEU cc_start: 0.8253 (tp) cc_final: 0.7958 (tp) REVERT: B 144 MET cc_start: 0.5897 (ppp) cc_final: 0.5683 (ppp) REVERT: A 758 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7344 (mm-40) outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 0.1473 time to fit residues: 27.4402 Evaluate side-chains 73 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 674 GLN B 939 ASN A 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.073110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053402 restraints weight = 121020.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054187 restraints weight = 70896.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054356 restraints weight = 46117.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054755 restraints weight = 45371.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054780 restraints weight = 38278.930| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26103 Z= 0.202 Angle : 0.590 7.998 35570 Z= 0.312 Chirality : 0.044 0.185 4017 Planarity : 0.004 0.069 4613 Dihedral : 4.514 49.018 3510 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 0.28 % Allowed : 7.12 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3245 helix: 1.41 (0.21), residues: 683 sheet: -1.01 (0.22), residues: 592 loop : -1.72 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 448 TYR 0.020 0.001 TYR C 260 PHE 0.018 0.001 PHE A 383 TRP 0.015 0.001 TRP A 143 HIS 0.004 0.001 HIS C 646 Details of bonding type rmsd covalent geometry : bond 0.00453 (26064) covalent geometry : angle 0.58749 (35492) SS BOND : bond 0.00404 ( 39) SS BOND : angle 1.33562 ( 78) hydrogen bonds : bond 0.04853 ( 768) hydrogen bonds : angle 6.70765 ( 2127) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.960 Fit side-chains REVERT: B 108 LEU cc_start: 0.8629 (tp) cc_final: 0.8408 (tp) REVERT: B 168 MET cc_start: 0.2330 (mmp) cc_final: 0.1955 (mmp) REVERT: B 378 LEU cc_start: 0.8971 (mt) cc_final: 0.8749 (mt) REVERT: B 532 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: B 884 MET cc_start: 0.8989 (mmt) cc_final: 0.8788 (mmm) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1466 time to fit residues: 20.8005 Evaluate side-chains 74 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 100 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 125 optimal weight: 40.0000 chunk 206 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 571 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 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 = 0.3631 r_free = 0.3631 target = 0.072530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052870 restraints weight = 121163.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053430 restraints weight = 69097.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053737 restraints weight = 46283.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.053909 restraints weight = 43650.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.053998 restraints weight = 38945.984| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26103 Z= 0.196 Angle : 0.579 8.253 35570 Z= 0.304 Chirality : 0.043 0.166 4017 Planarity : 0.004 0.058 4613 Dihedral : 4.677 55.208 3510 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 0.85 % Allowed : 11.49 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3245 helix: 1.25 (0.20), residues: 692 sheet: -1.16 (0.21), residues: 627 loop : -1.74 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 448 TYR 0.025 0.002 TYR B1094 PHE 0.026 0.001 PHE B 368 TRP 0.011 0.001 TRP A 143 HIS 0.004 0.001 HIS C 646 Details of bonding type rmsd covalent geometry : bond 0.00445 (26064) covalent geometry : angle 0.57535 (35492) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.42506 ( 78) hydrogen bonds : bond 0.04045 ( 768) hydrogen bonds : angle 6.13260 ( 2127) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: B 108 LEU cc_start: 0.8661 (tp) cc_final: 0.8434 (tp) REVERT: B 168 MET cc_start: 0.2714 (mmp) cc_final: 0.2330 (mmp) REVERT: B 378 LEU cc_start: 0.8914 (mt) cc_final: 0.8677 (mt) REVERT: B 532 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: B 1094 TYR cc_start: 0.8474 (t80) cc_final: 0.8232 (t80) REVERT: A 136 TYR cc_start: 0.5249 (m-80) cc_final: 0.5040 (m-80) outliers start: 24 outliers final: 16 residues processed: 97 average time/residue: 0.1367 time to fit residues: 23.2046 Evaluate side-chains 85 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 757 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 258 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 155 optimal weight: 0.0970 chunk 218 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 986 GLN A 128 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 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 = 0.3620 r_free = 0.3620 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052660 restraints weight = 121028.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052917 restraints weight = 73646.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053394 restraints weight = 48490.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053496 restraints weight = 45736.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053720 restraints weight = 39487.962| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 26103 Z= 0.208 Angle : 0.583 8.319 35570 Z= 0.306 Chirality : 0.043 0.152 4017 Planarity : 0.004 0.058 4613 Dihedral : 4.730 52.318 3510 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.03 % Favored : 90.91 % Rotamer: Outliers : 1.48 % Allowed : 13.39 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.15), residues: 3245 helix: 1.18 (0.20), residues: 692 sheet: -1.27 (0.21), residues: 632 loop : -1.80 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 448 TYR 0.018 0.002 TYR C1051 PHE 0.015 0.001 PHE A 383 TRP 0.017 0.001 TRP B 249 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00469 (26064) covalent geometry : angle 0.57960 (35492) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.42645 ( 78) hydrogen bonds : bond 0.03911 ( 768) hydrogen bonds : angle 5.98368 ( 2127) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 71 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: C 562 ASP cc_start: 0.6265 (t0) cc_final: 0.6052 (t70) REVERT: B 108 LEU cc_start: 0.8782 (tp) cc_final: 0.8530 (tp) REVERT: B 168 MET cc_start: 0.2667 (mmp) cc_final: 0.2253 (mmp) REVERT: B 378 LEU cc_start: 0.8915 (mt) cc_final: 0.8609 (mt) REVERT: B 532 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: A 136 TYR cc_start: 0.5453 (m-80) cc_final: 0.5201 (m-80) REVERT: A 353 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (m) outliers start: 42 outliers final: 27 residues processed: 110 average time/residue: 0.1562 time to fit residues: 29.5999 Evaluate side-chains 94 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 1088 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 177 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 267 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A1020 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053262 restraints weight = 119428.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053725 restraints weight = 71743.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054264 restraints weight = 45595.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.054369 restraints weight = 42967.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054513 restraints weight = 37249.443| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26103 Z= 0.142 Angle : 0.546 8.411 35570 Z= 0.286 Chirality : 0.042 0.257 4017 Planarity : 0.004 0.057 4613 Dihedral : 4.629 57.141 3510 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 1.73 % Allowed : 14.66 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3245 helix: 1.35 (0.20), residues: 688 sheet: -1.17 (0.20), residues: 647 loop : -1.76 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 448 TYR 0.016 0.001 TYR C1051 PHE 0.016 0.001 PHE C 583 TRP 0.023 0.001 TRP A 624 HIS 0.003 0.001 HIS C1067 Details of bonding type rmsd covalent geometry : bond 0.00326 (26064) covalent geometry : angle 0.53997 (35492) SS BOND : bond 0.00359 ( 39) SS BOND : angle 1.78305 ( 78) hydrogen bonds : bond 0.03631 ( 768) hydrogen bonds : angle 5.69711 ( 2127) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 66 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: B 168 MET cc_start: 0.2534 (mmp) cc_final: 0.2169 (mmp) REVERT: B 378 LEU cc_start: 0.8954 (mt) cc_final: 0.8645 (mt) REVERT: B 532 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: A 136 TYR cc_start: 0.5355 (m-80) cc_final: 0.5127 (m-80) REVERT: A 353 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8527 (m) REVERT: A 507 GLU cc_start: 0.7325 (pm20) cc_final: 0.6940 (pt0) REVERT: A 853 MET cc_start: 0.8493 (ptp) cc_final: 0.8015 (mtp) outliers start: 49 outliers final: 35 residues processed: 114 average time/residue: 0.1472 time to fit residues: 29.1451 Evaluate side-chains 103 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 757 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 19 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 103 optimal weight: 0.3980 chunk 277 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 527 ASN C1072 HIS C1085 HIS ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 400 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.070724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051431 restraints weight = 121963.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051561 restraints weight = 77298.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051771 restraints weight = 56077.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051931 restraints weight = 53195.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052055 restraints weight = 46206.516| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 26103 Z= 0.320 Angle : 0.691 12.082 35570 Z= 0.362 Chirality : 0.045 0.238 4017 Planarity : 0.005 0.060 4613 Dihedral : 5.058 50.741 3510 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.66 % Favored : 89.28 % Rotamer: Outliers : 2.64 % Allowed : 15.47 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.14), residues: 3245 helix: 0.73 (0.19), residues: 704 sheet: -1.29 (0.20), residues: 658 loop : -1.96 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 448 TYR 0.022 0.002 TYR C1051 PHE 0.019 0.002 PHE A 383 TRP 0.046 0.002 TRP A 624 HIS 0.006 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00720 (26064) covalent geometry : angle 0.68474 (35492) SS BOND : bond 0.00412 ( 39) SS BOND : angle 2.14115 ( 78) hydrogen bonds : bond 0.04338 ( 768) hydrogen bonds : angle 6.14054 ( 2127) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 70 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: C 1013 MET cc_start: 0.8574 (tpp) cc_final: 0.7953 (ttm) REVERT: B 378 LEU cc_start: 0.8877 (mt) cc_final: 0.8554 (mt) REVERT: B 532 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: B 711 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8747 (mm) REVERT: A 136 TYR cc_start: 0.5127 (m-80) cc_final: 0.4924 (m-80) REVERT: A 353 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8500 (m) REVERT: A 885 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8902 (tt0) outliers start: 75 outliers final: 51 residues processed: 142 average time/residue: 0.1526 time to fit residues: 37.3736 Evaluate side-chains 120 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 65 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1061 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 98 optimal weight: 0.9980 chunk 249 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1072 HIS ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A 939 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.072831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053279 restraints weight = 120125.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053689 restraints weight = 73844.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054257 restraints weight = 47822.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.054389 restraints weight = 43486.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.054650 restraints weight = 38469.950| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26103 Z= 0.122 Angle : 0.556 11.824 35570 Z= 0.291 Chirality : 0.043 0.209 4017 Planarity : 0.004 0.057 4613 Dihedral : 4.765 56.870 3510 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.37 % Favored : 92.57 % Rotamer: Outliers : 2.04 % Allowed : 16.17 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 3245 helix: 1.14 (0.20), residues: 702 sheet: -1.19 (0.20), residues: 651 loop : -1.84 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 448 TYR 0.016 0.001 TYR B1051 PHE 0.014 0.001 PHE C 583 TRP 0.053 0.001 TRP A 624 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00281 (26064) covalent geometry : angle 0.55074 (35492) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.74348 ( 78) hydrogen bonds : bond 0.03610 ( 768) hydrogen bonds : angle 5.58058 ( 2127) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 76 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.5315 (pmm) cc_final: 0.4555 (pmm) REVERT: C 1013 MET cc_start: 0.8418 (tpp) cc_final: 0.7909 (ttm) REVERT: B 168 MET cc_start: 0.2158 (mmp) cc_final: 0.1908 (mmp) REVERT: B 378 LEU cc_start: 0.8956 (mt) cc_final: 0.8638 (mt) REVERT: B 532 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: B 888 TYR cc_start: 0.7562 (m-10) cc_final: 0.7279 (m-80) REVERT: A 136 TYR cc_start: 0.5371 (m-80) cc_final: 0.5130 (m-80) REVERT: A 215 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (pp20) REVERT: A 353 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8510 (m) REVERT: A 624 TRP cc_start: 0.5319 (OUTLIER) cc_final: 0.5032 (p90) outliers start: 58 outliers final: 34 residues processed: 131 average time/residue: 0.1455 time to fit residues: 32.9305 Evaluate side-chains 106 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 1015 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1072 HIS ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.071164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052289 restraints weight = 122134.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052187 restraints weight = 81447.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052357 restraints weight = 60553.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052543 restraints weight = 53205.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052648 restraints weight = 48503.874| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 26103 Z= 0.259 Angle : 0.633 9.970 35570 Z= 0.331 Chirality : 0.044 0.172 4017 Planarity : 0.004 0.058 4613 Dihedral : 4.929 52.691 3510 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer: Outliers : 2.33 % Allowed : 16.38 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3245 helix: 0.94 (0.20), residues: 703 sheet: -1.25 (0.20), residues: 642 loop : -1.93 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 889 TYR 0.023 0.002 TYR C 665 PHE 0.035 0.002 PHE C 420 TRP 0.051 0.002 TRP A 624 HIS 0.005 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00587 (26064) covalent geometry : angle 0.62842 (35492) SS BOND : bond 0.00385 ( 39) SS BOND : angle 1.77883 ( 78) hydrogen bonds : bond 0.04000 ( 768) hydrogen bonds : angle 5.84797 ( 2127) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 69 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: C 1013 MET cc_start: 0.8573 (tpp) cc_final: 0.8009 (ttm) REVERT: B 168 MET cc_start: 0.1841 (mmp) cc_final: 0.1515 (mmp) REVERT: B 378 LEU cc_start: 0.8892 (mt) cc_final: 0.8571 (mt) REVERT: B 532 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: B 888 TYR cc_start: 0.7592 (m-10) cc_final: 0.7278 (m-80) REVERT: A 136 TYR cc_start: 0.5260 (m-80) cc_final: 0.5027 (m-80) REVERT: A 215 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8256 (pp20) REVERT: A 353 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8460 (m) REVERT: A 885 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8872 (tt0) outliers start: 66 outliers final: 50 residues processed: 133 average time/residue: 0.1465 time to fit residues: 33.6732 Evaluate side-chains 122 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 68 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1045 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.072248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053212 restraints weight = 121514.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053222 restraints weight = 75594.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053740 restraints weight = 50085.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053885 restraints weight = 43379.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053973 restraints weight = 39521.597| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26103 Z= 0.149 Angle : 0.573 10.746 35570 Z= 0.298 Chirality : 0.043 0.172 4017 Planarity : 0.004 0.058 4613 Dihedral : 4.802 55.957 3510 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 1.94 % Allowed : 16.98 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 3245 helix: 1.08 (0.20), residues: 705 sheet: -1.27 (0.20), residues: 645 loop : -1.88 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 399 TYR 0.019 0.001 TYR C 665 PHE 0.014 0.001 PHE C 583 TRP 0.054 0.001 TRP A 624 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00344 (26064) covalent geometry : angle 0.56755 (35492) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.71113 ( 78) hydrogen bonds : bond 0.03625 ( 768) hydrogen bonds : angle 5.56946 ( 2127) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 71 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: C 448 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5376 (pmt170) REVERT: C 1013 MET cc_start: 0.8475 (tpp) cc_final: 0.7937 (ttm) REVERT: B 168 MET cc_start: 0.1888 (mmp) cc_final: 0.1609 (mmp) REVERT: B 378 LEU cc_start: 0.8942 (mt) cc_final: 0.8627 (mt) REVERT: B 888 TYR cc_start: 0.7552 (m-10) cc_final: 0.7204 (m-10) REVERT: A 136 TYR cc_start: 0.5328 (m-80) cc_final: 0.5113 (m-80) REVERT: A 215 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8262 (pp20) REVERT: A 353 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8531 (m) outliers start: 55 outliers final: 47 residues processed: 125 average time/residue: 0.1366 time to fit residues: 29.8596 Evaluate side-chains 117 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 67 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1045 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 202 optimal weight: 0.7980 chunk 249 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 239 optimal weight: 30.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 944 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.071804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052900 restraints weight = 121825.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052963 restraints weight = 69107.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053375 restraints weight = 51122.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053484 restraints weight = 45801.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053589 restraints weight = 40212.651| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26103 Z= 0.187 Angle : 0.593 9.544 35570 Z= 0.307 Chirality : 0.043 0.177 4017 Planarity : 0.004 0.058 4613 Dihedral : 4.822 54.611 3510 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.12 % Favored : 90.82 % Rotamer: Outliers : 2.15 % Allowed : 16.98 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3245 helix: 1.01 (0.20), residues: 705 sheet: -1.25 (0.20), residues: 647 loop : -1.89 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 448 TYR 0.020 0.001 TYR C 665 PHE 0.021 0.001 PHE A 124 TRP 0.046 0.002 TRP A 624 HIS 0.003 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00427 (26064) covalent geometry : angle 0.58739 (35492) SS BOND : bond 0.00364 ( 39) SS BOND : angle 1.82072 ( 78) hydrogen bonds : bond 0.03702 ( 768) hydrogen bonds : angle 5.62675 ( 2127) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 71 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: C 448 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5510 (pmt170) REVERT: C 1013 MET cc_start: 0.8516 (tpp) cc_final: 0.7998 (ttm) REVERT: B 168 MET cc_start: 0.1973 (mmp) cc_final: 0.1680 (mmp) REVERT: B 207 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6648 (mt) REVERT: B 378 LEU cc_start: 0.8917 (mt) cc_final: 0.8613 (mt) REVERT: B 888 TYR cc_start: 0.7564 (m-10) cc_final: 0.7228 (m-80) REVERT: A 215 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8278 (pp20) outliers start: 61 outliers final: 54 residues processed: 130 average time/residue: 0.1440 time to fit residues: 32.6061 Evaluate side-chains 125 residues out of total 2842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 68 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 722 CYS Chi-restraints excluded: chain B residue 857 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1112 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1045 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 151 optimal weight: 5.9990 chunk 240 optimal weight: 40.0000 chunk 323 optimal weight: 5.9990 chunk 3 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.071935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052893 restraints weight = 121222.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052951 restraints weight = 74480.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053404 restraints weight = 51648.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053554 restraints weight = 46368.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053642 restraints weight = 40863.996| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26103 Z= 0.180 Angle : 0.589 10.865 35570 Z= 0.306 Chirality : 0.043 0.192 4017 Planarity : 0.004 0.058 4613 Dihedral : 4.810 55.031 3510 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.06 % Favored : 90.88 % Rotamer: Outliers : 2.11 % Allowed : 17.12 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3245 helix: 1.06 (0.20), residues: 701 sheet: -1.25 (0.21), residues: 637 loop : -1.91 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 448 TYR 0.020 0.001 TYR C 665 PHE 0.021 0.001 PHE A 124 TRP 0.037 0.001 TRP A 624 HIS 0.003 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00412 (26064) covalent geometry : angle 0.58269 (35492) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.87484 ( 78) hydrogen bonds : bond 0.03664 ( 768) hydrogen bonds : angle 5.58847 ( 2127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3194.26 seconds wall clock time: 56 minutes 41.89 seconds (3401.89 seconds total)