Starting phenix.real_space_refine on Thu Mar 5 17:06:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwl_23549/03_2026/7lwl_23549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwl_23549/03_2026/7lwl_23549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwl_23549/03_2026/7lwl_23549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwl_23549/03_2026/7lwl_23549.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwl_23549/03_2026/7lwl_23549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwl_23549/03_2026/7lwl_23549.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.097 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 105 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 23847 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.22, per 1000 atoms: 0.22 Number of scatterers: 23847 At special positions: 0 Unit cell: (135.763, 129.349, 175.316, 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 105 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 988.7 milliseconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 27.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.727A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.583A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.911A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.950A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.801A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.611A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.662A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.143A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.077A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.576A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.652A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.201A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.611A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.814A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.604A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.610A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.179A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.622A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.102A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.808A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.091A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.784A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.541A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.805A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.580A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.270A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.756A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.088A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.088A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 96 removed outlier: 4.402A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.989A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.843A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.660A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.829A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.501A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.107A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.604A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.591A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.993A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.001A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.493A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.779A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.496A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.801A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.696A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.958A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.633A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.138A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.843A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.203A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.878A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.512A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.813A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.603A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.571A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2880 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: 5.57 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6493 1.33 - 1.46: 4441 1.46 - 1.58: 13303 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 24366 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.62e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.56e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 24361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 23208 1.82 - 3.64: 8464 3.64 - 5.46: 1344 5.46 - 7.28: 112 7.28 - 9.10: 16 Bond angle restraints: 33144 Sorted by residual: angle pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " pdb=" CG PHE A 86 " ideal model delta sigma weight residual 113.80 121.24 -7.44 1.00e+00 1.00e+00 5.54e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" CA PHE A 194 " pdb=" CB PHE A 194 " pdb=" CG PHE A 194 " ideal model delta sigma weight residual 113.80 119.68 -5.88 1.00e+00 1.00e+00 3.45e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 119.68 -5.88 1.00e+00 1.00e+00 3.45e+01 angle pdb=" CA PHE C 186 " pdb=" CB PHE C 186 " pdb=" CG PHE C 186 " ideal model delta sigma weight residual 113.80 119.65 -5.85 1.00e+00 1.00e+00 3.42e+01 ... (remaining 33139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 13907 17.51 - 35.03: 772 35.03 - 52.54: 141 52.54 - 70.06: 56 70.06 - 87.57: 31 Dihedral angle restraints: 14907 sinusoidal: 6180 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.53 73.53 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.60 67.60 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CA THR A 599 " pdb=" C THR A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 14904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2465 0.089 - 0.178: 1206 0.178 - 0.268: 178 0.268 - 0.357: 26 0.357 - 0.446: 1 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA THR A 108 " pdb=" N THR A 108 " pdb=" C THR A 108 " pdb=" CB THR A 108 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA ASP A 745 " pdb=" N ASP A 745 " pdb=" C ASP A 745 " pdb=" CB ASP A 745 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA ASN A 487 " pdb=" N ASN A 487 " pdb=" C ASN A 487 " pdb=" CB ASN A 487 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.141 2.00e-02 2.50e+03 1.50e-01 2.82e+02 pdb=" CG ASN A 603 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 91 " -0.207 2.00e-02 2.50e+03 1.07e-01 2.30e+02 pdb=" CG TYR A 91 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 TYR A 91 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TYR A 91 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 TYR A 91 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 91 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 91 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 91 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.122 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" CG ASN A 709 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " -0.153 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 11063 2.98 - 3.46: 22327 3.46 - 3.94: 39962 3.94 - 4.42: 44189 4.42 - 4.90: 75325 Nonbonded interactions: 192866 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.508 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.516 3.040 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.518 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.527 3.040 ... (remaining 192861 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 23.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.013 0.077 24435 Z= 0.773 Angle : 1.807 9.099 33312 Z= 1.208 Chirality : 0.096 0.446 3876 Planarity : 0.013 0.158 4251 Dihedral : 12.808 87.572 9168 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.53 % Allowed : 2.14 % Favored : 97.33 % Cbeta Deviations : 0.07 % 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: -0.78 (0.14), residues: 2955 helix: -0.82 (0.17), residues: 687 sheet: 0.36 (0.22), residues: 505 loop : -0.61 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1019 TYR 0.207 0.022 TYR A 91 PHE 0.098 0.012 PHE B 718 TRP 0.113 0.022 TRP C 104 HIS 0.009 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.01331 (24366) covalent geometry : angle 1.79243 (33144) SS BOND : bond 0.01343 ( 39) SS BOND : angle 2.35263 ( 78) hydrogen bonds : bond 0.16465 ( 1045) hydrogen bonds : angle 8.18257 ( 2880) link_NAG-ASN : bond 0.01174 ( 30) link_NAG-ASN : angle 4.46897 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 366 time to evaluate : 0.801 Fit side-chains REVERT: A 129 LYS cc_start: 0.6298 (mttm) cc_final: 0.5990 (mppt) REVERT: A 278 LYS cc_start: 0.8327 (tttt) cc_final: 0.8065 (ttpt) REVERT: A 569 ILE cc_start: 0.7914 (mm) cc_final: 0.7711 (mp) REVERT: A 586 ASP cc_start: 0.6859 (t70) cc_final: 0.5886 (m-30) REVERT: A 697 MET cc_start: 0.9140 (ptm) cc_final: 0.8853 (ptm) REVERT: A 731 MET cc_start: 0.9296 (ptt) cc_final: 0.8871 (ptt) REVERT: A 1029 MET cc_start: 0.9294 (tpp) cc_final: 0.8606 (tpp) REVERT: B 32 PHE cc_start: 0.6822 (m-80) cc_final: 0.6382 (m-10) REVERT: B 271 GLN cc_start: 0.7844 (mt0) cc_final: 0.7637 (mm-40) REVERT: B 334 ASN cc_start: 0.6781 (m-40) cc_final: 0.6515 (p0) REVERT: B 357 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7508 (ttt-90) REVERT: B 359 SER cc_start: 0.8615 (p) cc_final: 0.8189 (m) REVERT: C 81 ASN cc_start: 0.7737 (p0) cc_final: 0.7193 (p0) REVERT: C 121 ASN cc_start: 0.7331 (t0) cc_final: 0.6943 (m-40) REVERT: C 237 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7739 (mtp85) REVERT: C 369 TYR cc_start: 0.6924 (p90) cc_final: 0.6372 (t80) REVERT: C 378 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7548 (tttp) REVERT: C 403 ARG cc_start: 0.6875 (ptt-90) cc_final: 0.6577 (ptm-80) REVERT: C 405 ASP cc_start: 0.7191 (m-30) cc_final: 0.6496 (m-30) REVERT: C 417 LYS cc_start: 0.8125 (mttt) cc_final: 0.7754 (mmtt) REVERT: C 529 LYS cc_start: 0.8178 (mttt) cc_final: 0.7962 (tppt) REVERT: C 646 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7385 (ttp80) REVERT: C 1017 GLU cc_start: 0.7602 (tt0) cc_final: 0.7364 (tt0) outliers start: 14 outliers final: 6 residues processed: 378 average time/residue: 0.5734 time to fit residues: 251.1829 Evaluate side-chains 214 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 519 HIS A 755 GLN A 764 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 540 ASN B 607 GLN B 675 GLN B1010 GLN C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 506 GLN C 540 ASN C 690 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.192874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125552 restraints weight = 28024.366| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.37 r_work: 0.3228 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24435 Z= 0.140 Angle : 0.671 13.215 33312 Z= 0.350 Chirality : 0.047 0.189 3876 Planarity : 0.004 0.040 4251 Dihedral : 6.159 45.289 3838 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.06 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 7.09 % Favored : 90.81 % 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: 0.29 (0.15), residues: 2955 helix: 1.32 (0.20), residues: 682 sheet: 0.36 (0.19), residues: 654 loop : -0.32 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.025 0.002 TYR C 369 PHE 0.026 0.002 PHE B 453 TRP 0.029 0.002 TRP B 64 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00301 (24366) covalent geometry : angle 0.64172 (33144) SS BOND : bond 0.00577 ( 39) SS BOND : angle 1.58364 ( 78) hydrogen bonds : bond 0.04975 ( 1045) hydrogen bonds : angle 6.20628 ( 2880) link_NAG-ASN : bond 0.00205 ( 30) link_NAG-ASN : angle 3.59832 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6259 (mttm) cc_final: 0.5902 (mppt) REVERT: A 278 LYS cc_start: 0.8739 (tttt) cc_final: 0.8469 (ttmm) REVERT: A 281 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8041 (pp20) REVERT: A 347 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.4047 (t80) REVERT: A 355 ARG cc_start: 0.7610 (ttt180) cc_final: 0.7226 (tpp80) REVERT: A 568 ASP cc_start: 0.7450 (m-30) cc_final: 0.7178 (m-30) REVERT: A 569 ILE cc_start: 0.7551 (mm) cc_final: 0.7269 (mm) REVERT: A 586 ASP cc_start: 0.6810 (t70) cc_final: 0.5716 (m-30) REVERT: A 731 MET cc_start: 0.9402 (ptt) cc_final: 0.9083 (ptt) REVERT: A 964 LYS cc_start: 0.8708 (mttt) cc_final: 0.8397 (mtpt) REVERT: A 1029 MET cc_start: 0.9291 (tpp) cc_final: 0.8813 (tpp) REVERT: B 32 PHE cc_start: 0.6656 (m-80) cc_final: 0.6328 (m-10) REVERT: B 271 GLN cc_start: 0.7941 (mt0) cc_final: 0.7667 (mm-40) REVERT: B 323 THR cc_start: 0.8144 (m) cc_final: 0.7575 (p) REVERT: B 334 ASN cc_start: 0.6326 (m-40) cc_final: 0.5798 (p0) REVERT: B 359 SER cc_start: 0.8830 (p) cc_final: 0.8396 (m) REVERT: B 935 GLN cc_start: 0.7920 (mt0) cc_final: 0.7584 (tt0) REVERT: B 985 ASP cc_start: 0.7610 (p0) cc_final: 0.7365 (p0) REVERT: B 988 GLU cc_start: 0.7585 (mp0) cc_final: 0.7368 (mp0) REVERT: C 81 ASN cc_start: 0.8044 (p0) cc_final: 0.7260 (p0) REVERT: C 121 ASN cc_start: 0.7435 (t0) cc_final: 0.7071 (m-40) REVERT: C 170 TYR cc_start: 0.7825 (t80) cc_final: 0.7592 (t80) REVERT: C 188 ASN cc_start: 0.5849 (m110) cc_final: 0.5158 (p0) REVERT: C 200 TYR cc_start: 0.7974 (m-80) cc_final: 0.7612 (m-80) REVERT: C 205 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8706 (t) REVERT: C 237 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7657 (mtm180) REVERT: C 369 TYR cc_start: 0.7014 (p90) cc_final: 0.6463 (t80) REVERT: C 375 SER cc_start: 0.7763 (m) cc_final: 0.7517 (p) REVERT: C 378 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7465 (tttp) REVERT: C 393 THR cc_start: 0.8083 (m) cc_final: 0.7874 (p) REVERT: C 405 ASP cc_start: 0.7428 (m-30) cc_final: 0.7184 (m-30) REVERT: C 452 LEU cc_start: 0.8205 (mp) cc_final: 0.7702 (mm) REVERT: C 505 TYR cc_start: 0.7288 (m-80) cc_final: 0.6638 (t80) REVERT: C 529 LYS cc_start: 0.8337 (mttt) cc_final: 0.7840 (tppt) REVERT: C 572 THR cc_start: 0.8731 (p) cc_final: 0.8527 (t) REVERT: C 574 ASP cc_start: 0.8425 (t70) cc_final: 0.8100 (t0) REVERT: C 776 LYS cc_start: 0.8857 (tttt) cc_final: 0.8575 (ttpp) REVERT: C 804 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: C 1017 GLU cc_start: 0.8538 (tt0) cc_final: 0.8279 (tt0) outliers start: 55 outliers final: 21 residues processed: 281 average time/residue: 0.5224 time to fit residues: 172.6261 Evaluate side-chains 212 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 256 optimal weight: 7.9990 chunk 272 optimal weight: 0.3980 chunk 13 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 613 GLN A1010 GLN B 49 HIS B 196 ASN B 394 ASN B 498 GLN B 501 ASN B 907 ASN B 913 GLN C 207 HIS C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.192778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125544 restraints weight = 28090.583| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.37 r_work: 0.3224 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24435 Z= 0.118 Angle : 0.593 13.701 33312 Z= 0.303 Chirality : 0.046 0.335 3876 Planarity : 0.004 0.045 4251 Dihedral : 5.873 64.902 3835 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 2.06 % Allowed : 8.85 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.51 (0.15), residues: 2955 helix: 1.93 (0.21), residues: 674 sheet: 0.37 (0.19), residues: 645 loop : -0.31 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.022 0.001 TYR C 369 PHE 0.027 0.001 PHE B 453 TRP 0.024 0.001 TRP B 64 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00250 (24366) covalent geometry : angle 0.57373 (33144) SS BOND : bond 0.00708 ( 39) SS BOND : angle 1.22085 ( 78) hydrogen bonds : bond 0.04227 ( 1045) hydrogen bonds : angle 5.75478 ( 2880) link_NAG-ASN : bond 0.00819 ( 30) link_NAG-ASN : angle 2.75839 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6322 (mttm) cc_final: 0.6059 (mppt) REVERT: A 278 LYS cc_start: 0.8776 (tttt) cc_final: 0.8445 (ttmm) REVERT: A 281 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: A 355 ARG cc_start: 0.7607 (ttt180) cc_final: 0.7277 (tpp80) REVERT: A 400 PHE cc_start: 0.6392 (p90) cc_final: 0.5722 (p90) REVERT: A 569 ILE cc_start: 0.7580 (mm) cc_final: 0.7264 (mm) REVERT: A 586 ASP cc_start: 0.6876 (t70) cc_final: 0.5724 (m-30) REVERT: A 731 MET cc_start: 0.9418 (ptt) cc_final: 0.9072 (ptt) REVERT: A 780 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8167 (pt0) REVERT: A 964 LYS cc_start: 0.8673 (mttt) cc_final: 0.8395 (mtpt) REVERT: A 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.8748 (tpp) REVERT: B 32 PHE cc_start: 0.6723 (m-80) cc_final: 0.6326 (m-10) REVERT: B 271 GLN cc_start: 0.7959 (mt0) cc_final: 0.7672 (mm-40) REVERT: B 323 THR cc_start: 0.8141 (m) cc_final: 0.7658 (p) REVERT: B 811 LYS cc_start: 0.6826 (mmtt) cc_final: 0.6480 (mppt) REVERT: B 900 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8669 (mtm) REVERT: B 916 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (tt) REVERT: B 935 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 985 ASP cc_start: 0.7617 (p0) cc_final: 0.7362 (p0) REVERT: B 988 GLU cc_start: 0.7487 (mp0) cc_final: 0.6985 (mp0) REVERT: C 81 ASN cc_start: 0.8041 (p0) cc_final: 0.7287 (p0) REVERT: C 121 ASN cc_start: 0.7360 (t0) cc_final: 0.7015 (m-40) REVERT: C 170 TYR cc_start: 0.7901 (t80) cc_final: 0.7672 (t80) REVERT: C 188 ASN cc_start: 0.5961 (m110) cc_final: 0.5325 (p0) REVERT: C 200 TYR cc_start: 0.7940 (m-80) cc_final: 0.7489 (m-80) REVERT: C 237 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7698 (mtm180) REVERT: C 369 TYR cc_start: 0.6935 (p90) cc_final: 0.6454 (t80) REVERT: C 378 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7430 (tttp) REVERT: C 393 THR cc_start: 0.8323 (m) cc_final: 0.8069 (p) REVERT: C 405 ASP cc_start: 0.7272 (m-30) cc_final: 0.6954 (m-30) REVERT: C 452 LEU cc_start: 0.8128 (mp) cc_final: 0.7691 (mm) REVERT: C 453 PHE cc_start: 0.7666 (p90) cc_final: 0.7349 (p90) REVERT: C 505 TYR cc_start: 0.7426 (m-80) cc_final: 0.6784 (t80) REVERT: C 506 GLN cc_start: 0.7426 (mt0) cc_final: 0.7171 (mt0) REVERT: C 529 LYS cc_start: 0.8421 (mttt) cc_final: 0.7880 (tppt) REVERT: C 572 THR cc_start: 0.8767 (p) cc_final: 0.8547 (t) REVERT: C 574 ASP cc_start: 0.8355 (t70) cc_final: 0.8114 (t0) REVERT: C 994 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: C 1017 GLU cc_start: 0.8574 (tt0) cc_final: 0.8338 (tt0) outliers start: 54 outliers final: 25 residues processed: 257 average time/residue: 0.5072 time to fit residues: 154.6539 Evaluate side-chains 224 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 35 optimal weight: 0.0060 chunk 204 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 243 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 145 optimal weight: 2.9990 chunk 299 optimal weight: 0.0010 chunk 93 optimal weight: 1.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A1010 GLN B 196 ASN B 394 ASN B1010 GLN C 196 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.197717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136998 restraints weight = 28399.431| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.56 r_work: 0.3383 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24435 Z= 0.094 Angle : 0.529 9.808 33312 Z= 0.271 Chirality : 0.044 0.230 3876 Planarity : 0.003 0.046 4251 Dihedral : 5.621 91.029 3835 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 1.79 % Allowed : 10.03 % Favored : 88.18 % 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: 0.72 (0.15), residues: 2955 helix: 2.28 (0.21), residues: 668 sheet: 0.43 (0.19), residues: 636 loop : -0.23 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.019 0.001 TYR C1067 PHE 0.029 0.001 PHE B 453 TRP 0.022 0.001 TRP B 64 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00192 (24366) covalent geometry : angle 0.51268 (33144) SS BOND : bond 0.00359 ( 39) SS BOND : angle 1.26648 ( 78) hydrogen bonds : bond 0.03507 ( 1045) hydrogen bonds : angle 5.42119 ( 2880) link_NAG-ASN : bond 0.00366 ( 30) link_NAG-ASN : angle 2.35400 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3775 (OUTLIER) cc_final: 0.3475 (mt) REVERT: A 129 LYS cc_start: 0.6322 (mttm) cc_final: 0.6070 (mppt) REVERT: A 278 LYS cc_start: 0.8757 (tttt) cc_final: 0.8386 (ttmm) REVERT: A 281 GLU cc_start: 0.8410 (pp20) cc_final: 0.8077 (pp20) REVERT: A 326 ILE cc_start: 0.6538 (mm) cc_final: 0.6304 (tt) REVERT: A 347 PHE cc_start: 0.4330 (OUTLIER) cc_final: 0.4080 (t80) REVERT: A 355 ARG cc_start: 0.7682 (ttt180) cc_final: 0.7413 (tpp80) REVERT: A 400 PHE cc_start: 0.6533 (p90) cc_final: 0.5946 (p90) REVERT: A 569 ILE cc_start: 0.7540 (mm) cc_final: 0.7202 (mm) REVERT: A 586 ASP cc_start: 0.6813 (t70) cc_final: 0.5783 (m-30) REVERT: A 603 ASN cc_start: 0.6832 (t0) cc_final: 0.6495 (t0) REVERT: A 731 MET cc_start: 0.9372 (ptt) cc_final: 0.9112 (ptt) REVERT: A 790 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8336 (ptpp) REVERT: A 964 LYS cc_start: 0.8536 (mttt) cc_final: 0.8331 (mtpt) REVERT: A 1029 MET cc_start: 0.8918 (tpp) cc_final: 0.8709 (tpp) REVERT: B 32 PHE cc_start: 0.6777 (m-80) cc_final: 0.6408 (m-10) REVERT: B 271 GLN cc_start: 0.7875 (mt0) cc_final: 0.7637 (mm-40) REVERT: B 323 THR cc_start: 0.8327 (m) cc_final: 0.7968 (p) REVERT: B 619 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: B 900 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8573 (mtm) REVERT: B 957 GLN cc_start: 0.8487 (tt0) cc_final: 0.8265 (tt0) REVERT: B 985 ASP cc_start: 0.7482 (p0) cc_final: 0.7258 (p0) REVERT: B 988 GLU cc_start: 0.7441 (mp0) cc_final: 0.7005 (mp0) REVERT: C 81 ASN cc_start: 0.8014 (p0) cc_final: 0.7314 (p0) REVERT: C 121 ASN cc_start: 0.7346 (t0) cc_final: 0.7067 (m-40) REVERT: C 170 TYR cc_start: 0.7865 (t80) cc_final: 0.7618 (t80) REVERT: C 188 ASN cc_start: 0.6061 (m110) cc_final: 0.5449 (p0) REVERT: C 200 TYR cc_start: 0.7900 (m-80) cc_final: 0.7509 (m-80) REVERT: C 237 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7667 (mtm180) REVERT: C 369 TYR cc_start: 0.6987 (p90) cc_final: 0.6435 (t80) REVERT: C 378 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7302 (tttp) REVERT: C 405 ASP cc_start: 0.7265 (m-30) cc_final: 0.7025 (m-30) REVERT: C 452 LEU cc_start: 0.8332 (mp) cc_final: 0.7931 (mm) REVERT: C 453 PHE cc_start: 0.7701 (p90) cc_final: 0.7337 (p90) REVERT: C 505 TYR cc_start: 0.7478 (m-80) cc_final: 0.6860 (t80) REVERT: C 506 GLN cc_start: 0.7603 (mt0) cc_final: 0.7401 (mt0) REVERT: C 529 LYS cc_start: 0.8392 (mttt) cc_final: 0.7876 (tppt) REVERT: C 581 THR cc_start: 0.8911 (m) cc_final: 0.8549 (p) REVERT: C 583 GLU cc_start: 0.8137 (pt0) cc_final: 0.7734 (pt0) REVERT: C 916 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8560 (tp) REVERT: C 994 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: C 1017 GLU cc_start: 0.8305 (tt0) cc_final: 0.8060 (tt0) REVERT: C 1145 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6655 (mt) outliers start: 47 outliers final: 14 residues processed: 248 average time/residue: 0.5285 time to fit residues: 154.5228 Evaluate side-chains 214 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 317 ASN A 354 ASN A 536 ASN A 901 GLN A1010 GLN B 196 ASN B 580 GLN B 901 GLN B 914 ASN B 935 GLN C 196 ASN C 207 HIS ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.192726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129414 restraints weight = 27980.391| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.53 r_work: 0.3288 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 24435 Z= 0.188 Angle : 0.602 9.865 33312 Z= 0.309 Chirality : 0.047 0.242 3876 Planarity : 0.004 0.051 4251 Dihedral : 5.847 100.472 3832 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 2.33 % Allowed : 10.14 % Favored : 87.53 % 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: 0.48 (0.15), residues: 2955 helix: 1.98 (0.21), residues: 667 sheet: 0.31 (0.19), residues: 645 loop : -0.35 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.021 0.002 TYR C1067 PHE 0.030 0.002 PHE B 453 TRP 0.022 0.002 TRP B 64 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00458 (24366) covalent geometry : angle 0.58524 (33144) SS BOND : bond 0.00385 ( 39) SS BOND : angle 1.48006 ( 78) hydrogen bonds : bond 0.04791 ( 1045) hydrogen bonds : angle 5.68142 ( 2880) link_NAG-ASN : bond 0.00337 ( 30) link_NAG-ASN : angle 2.44632 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6555 (mttm) cc_final: 0.6264 (mppt) REVERT: A 135 PHE cc_start: 0.6392 (t80) cc_final: 0.5921 (t80) REVERT: A 278 LYS cc_start: 0.8838 (tttt) cc_final: 0.8505 (ttmm) REVERT: A 281 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (pp20) REVERT: A 355 ARG cc_start: 0.7871 (ttt180) cc_final: 0.7590 (tpp80) REVERT: A 400 PHE cc_start: 0.6490 (p90) cc_final: 0.5974 (p90) REVERT: A 569 ILE cc_start: 0.7809 (mm) cc_final: 0.7501 (mm) REVERT: A 586 ASP cc_start: 0.6966 (t70) cc_final: 0.5931 (m-30) REVERT: A 603 ASN cc_start: 0.7246 (t0) cc_final: 0.6884 (t0) REVERT: A 731 MET cc_start: 0.9341 (ptt) cc_final: 0.9094 (ptt) REVERT: A 790 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8581 (ptpp) REVERT: A 1029 MET cc_start: 0.9131 (tpp) cc_final: 0.8926 (tpp) REVERT: B 32 PHE cc_start: 0.6669 (m-80) cc_final: 0.6376 (m-10) REVERT: B 271 GLN cc_start: 0.8019 (mt0) cc_final: 0.7737 (mm-40) REVERT: B 323 THR cc_start: 0.8420 (m) cc_final: 0.8090 (p) REVERT: B 740 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8328 (ttt) REVERT: B 900 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8669 (mtm) REVERT: B 988 GLU cc_start: 0.7530 (mp0) cc_final: 0.7235 (mp0) REVERT: C 81 ASN cc_start: 0.7914 (p0) cc_final: 0.6977 (p0) REVERT: C 121 ASN cc_start: 0.7430 (t0) cc_final: 0.7140 (m-40) REVERT: C 188 ASN cc_start: 0.5815 (m110) cc_final: 0.5107 (p0) REVERT: C 200 TYR cc_start: 0.8074 (m-80) cc_final: 0.7703 (m-80) REVERT: C 237 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7919 (mtm180) REVERT: C 239 GLN cc_start: 0.8202 (tt0) cc_final: 0.7950 (tt0) REVERT: C 269 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: C 281 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: C 369 TYR cc_start: 0.6979 (p90) cc_final: 0.6503 (t80) REVERT: C 378 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7529 (tttp) REVERT: C 405 ASP cc_start: 0.7293 (m-30) cc_final: 0.7080 (m-30) REVERT: C 453 PHE cc_start: 0.7726 (p90) cc_final: 0.7465 (p90) REVERT: C 505 TYR cc_start: 0.7402 (m-80) cc_final: 0.6750 (t80) REVERT: C 506 GLN cc_start: 0.7670 (mt0) cc_final: 0.7461 (mt0) REVERT: C 529 LYS cc_start: 0.8485 (mttt) cc_final: 0.8062 (tppt) REVERT: C 916 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8756 (tt) REVERT: C 994 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: C 1017 GLU cc_start: 0.8366 (tt0) cc_final: 0.8146 (tt0) REVERT: C 1145 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6805 (mt) outliers start: 61 outliers final: 24 residues processed: 241 average time/residue: 0.5210 time to fit residues: 148.5614 Evaluate side-chains 221 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 170 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A1010 GLN B 196 ASN B1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.191019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130036 restraints weight = 28094.262| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.75 r_work: 0.3258 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24435 Z= 0.245 Angle : 0.642 10.846 33312 Z= 0.330 Chirality : 0.049 0.262 3876 Planarity : 0.004 0.049 4251 Dihedral : 6.171 106.147 3832 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.56 % Allowed : 10.56 % Favored : 86.88 % 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: 0.26 (0.15), residues: 2955 helix: 1.76 (0.21), residues: 661 sheet: 0.24 (0.19), residues: 652 loop : -0.50 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 905 TYR 0.021 0.002 TYR A 91 PHE 0.032 0.002 PHE B 453 TRP 0.018 0.002 TRP B 64 HIS 0.006 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00604 (24366) covalent geometry : angle 0.62485 (33144) SS BOND : bond 0.00498 ( 39) SS BOND : angle 1.56513 ( 78) hydrogen bonds : bond 0.05178 ( 1045) hydrogen bonds : angle 5.82578 ( 2880) link_NAG-ASN : bond 0.00304 ( 30) link_NAG-ASN : angle 2.61411 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6052 (t80) cc_final: 0.5714 (t80) REVERT: A 281 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: A 347 PHE cc_start: 0.4838 (OUTLIER) cc_final: 0.4095 (t80) REVERT: A 355 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7639 (tpp80) REVERT: A 400 PHE cc_start: 0.6401 (p90) cc_final: 0.5641 (p90) REVERT: A 569 ILE cc_start: 0.8009 (mm) cc_final: 0.7685 (mm) REVERT: A 586 ASP cc_start: 0.6796 (t70) cc_final: 0.5746 (m-30) REVERT: A 603 ASN cc_start: 0.7286 (t0) cc_final: 0.6896 (t0) REVERT: A 619 GLU cc_start: 0.7716 (mp0) cc_final: 0.7497 (mp0) REVERT: A 731 MET cc_start: 0.9356 (ptt) cc_final: 0.9134 (ptt) REVERT: A 790 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8511 (ptpp) REVERT: A 1029 MET cc_start: 0.9222 (tpp) cc_final: 0.8956 (tpp) REVERT: B 32 PHE cc_start: 0.6606 (m-80) cc_final: 0.6302 (m-10) REVERT: B 271 GLN cc_start: 0.8017 (mt0) cc_final: 0.7779 (mm-40) REVERT: B 323 THR cc_start: 0.8447 (m) cc_final: 0.8138 (p) REVERT: B 335 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8585 (mp) REVERT: B 740 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8301 (ttt) REVERT: B 988 GLU cc_start: 0.7514 (mp0) cc_final: 0.7240 (mp0) REVERT: C 81 ASN cc_start: 0.7897 (p0) cc_final: 0.6928 (p0) REVERT: C 121 ASN cc_start: 0.7340 (t0) cc_final: 0.7085 (m-40) REVERT: C 200 TYR cc_start: 0.8029 (m-80) cc_final: 0.7756 (m-80) REVERT: C 237 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7828 (mtm180) REVERT: C 239 GLN cc_start: 0.8206 (tt0) cc_final: 0.7904 (tt0) REVERT: C 269 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: C 281 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: C 369 TYR cc_start: 0.6990 (p90) cc_final: 0.6441 (t80) REVERT: C 378 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7437 (tttp) REVERT: C 505 TYR cc_start: 0.7429 (m-80) cc_final: 0.6776 (t80) REVERT: C 529 LYS cc_start: 0.8481 (mttt) cc_final: 0.8032 (tppt) REVERT: C 916 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8811 (tt) REVERT: C 994 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: C 1017 GLU cc_start: 0.8371 (tt0) cc_final: 0.8092 (tt0) REVERT: C 1145 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6788 (mt) outliers start: 67 outliers final: 31 residues processed: 244 average time/residue: 0.5583 time to fit residues: 159.6005 Evaluate side-chains 230 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 9.9990 chunk 4 optimal weight: 0.0470 chunk 209 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 217 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 317 ASN A 354 ASN A 613 GLN A1010 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.194060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131436 restraints weight = 28022.954| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.49 r_work: 0.3321 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24435 Z= 0.113 Angle : 0.546 11.449 33312 Z= 0.280 Chirality : 0.045 0.248 3876 Planarity : 0.003 0.044 4251 Dihedral : 5.875 112.238 3832 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 1.64 % Allowed : 11.86 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 2955 helix: 2.20 (0.21), residues: 668 sheet: 0.35 (0.20), residues: 639 loop : -0.43 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.018 0.001 TYR C1067 PHE 0.033 0.001 PHE B 453 TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00257 (24366) covalent geometry : angle 0.52902 (33144) SS BOND : bond 0.00377 ( 39) SS BOND : angle 1.52706 ( 78) hydrogen bonds : bond 0.03974 ( 1045) hydrogen bonds : angle 5.50581 ( 2880) link_NAG-ASN : bond 0.00293 ( 30) link_NAG-ASN : angle 2.25576 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5971 (t80) cc_final: 0.5653 (t80) REVERT: A 281 GLU cc_start: 0.8500 (pp20) cc_final: 0.8235 (pp20) REVERT: A 347 PHE cc_start: 0.4760 (OUTLIER) cc_final: 0.4029 (t80) REVERT: A 400 PHE cc_start: 0.6437 (p90) cc_final: 0.5718 (p90) REVERT: A 569 ILE cc_start: 0.7875 (mm) cc_final: 0.7552 (mm) REVERT: A 586 ASP cc_start: 0.6931 (t70) cc_final: 0.5893 (m-30) REVERT: A 731 MET cc_start: 0.9350 (ptt) cc_final: 0.9082 (ptt) REVERT: A 1144 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8215 (mm-30) REVERT: B 32 PHE cc_start: 0.6523 (m-80) cc_final: 0.6217 (m-10) REVERT: B 271 GLN cc_start: 0.8115 (mt0) cc_final: 0.7744 (mm-40) REVERT: B 323 THR cc_start: 0.8475 (m) cc_final: 0.8234 (p) REVERT: B 740 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8324 (ttt) REVERT: C 28 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: C 81 ASN cc_start: 0.7938 (p0) cc_final: 0.6995 (p0) REVERT: C 200 TYR cc_start: 0.8025 (m-80) cc_final: 0.7667 (m-80) REVERT: C 237 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7814 (mtm180) REVERT: C 239 GLN cc_start: 0.8165 (tt0) cc_final: 0.7939 (tt0) REVERT: C 369 TYR cc_start: 0.7018 (p90) cc_final: 0.6482 (t80) REVERT: C 378 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7540 (tttp) REVERT: C 452 LEU cc_start: 0.8550 (mp) cc_final: 0.8070 (mm) REVERT: C 505 TYR cc_start: 0.7563 (m-80) cc_final: 0.6950 (t80) REVERT: C 529 LYS cc_start: 0.8474 (mttt) cc_final: 0.8039 (tppt) REVERT: C 574 ASP cc_start: 0.8172 (t0) cc_final: 0.7937 (m-30) REVERT: C 916 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8669 (tt) REVERT: C 994 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: C 1017 GLU cc_start: 0.8350 (tt0) cc_final: 0.8109 (tt0) REVERT: C 1145 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6831 (mt) outliers start: 43 outliers final: 21 residues processed: 230 average time/residue: 0.5265 time to fit residues: 142.8965 Evaluate side-chains 207 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 66 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 169 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A1010 GLN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.195702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133492 restraints weight = 28081.728| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.44 r_work: 0.3353 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24435 Z= 0.099 Angle : 0.522 12.345 33312 Z= 0.268 Chirality : 0.044 0.253 3876 Planarity : 0.003 0.045 4251 Dihedral : 5.718 115.437 3832 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Rotamer: Outliers : 1.56 % Allowed : 12.36 % Favored : 86.08 % 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: 0.68 (0.16), residues: 2955 helix: 2.37 (0.21), residues: 674 sheet: 0.42 (0.20), residues: 649 loop : -0.33 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.028 0.001 TYR C 170 PHE 0.034 0.001 PHE B 453 TRP 0.016 0.001 TRP B 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00219 (24366) covalent geometry : angle 0.50718 (33144) SS BOND : bond 0.00439 ( 39) SS BOND : angle 1.38482 ( 78) hydrogen bonds : bond 0.03587 ( 1045) hydrogen bonds : angle 5.28829 ( 2880) link_NAG-ASN : bond 0.00243 ( 30) link_NAG-ASN : angle 2.07030 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5991 (t80) cc_final: 0.5631 (t80) REVERT: A 281 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8155 (pp20) REVERT: A 347 PHE cc_start: 0.4828 (OUTLIER) cc_final: 0.4043 (t80) REVERT: A 354 ASN cc_start: 0.7247 (t0) cc_final: 0.6990 (t0) REVERT: A 400 PHE cc_start: 0.6475 (p90) cc_final: 0.5750 (p90) REVERT: A 569 ILE cc_start: 0.7845 (mm) cc_final: 0.7542 (mm) REVERT: A 586 ASP cc_start: 0.6793 (t70) cc_final: 0.5768 (m-30) REVERT: A 731 MET cc_start: 0.9369 (ptt) cc_final: 0.9082 (ptt) REVERT: A 1092 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8099 (mt-10) REVERT: B 32 PHE cc_start: 0.6481 (m-80) cc_final: 0.6187 (m-10) REVERT: B 271 GLN cc_start: 0.7986 (mt0) cc_final: 0.7636 (mt0) REVERT: B 740 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8208 (ttt) REVERT: B 916 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8795 (tp) REVERT: B 988 GLU cc_start: 0.7436 (mp0) cc_final: 0.6968 (mp0) REVERT: B 1118 ASP cc_start: 0.8584 (m-30) cc_final: 0.8335 (m-30) REVERT: C 81 ASN cc_start: 0.7935 (p0) cc_final: 0.6966 (p0) REVERT: C 200 TYR cc_start: 0.7949 (m-80) cc_final: 0.7566 (m-80) REVERT: C 237 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7711 (mtm180) REVERT: C 239 GLN cc_start: 0.8042 (tt0) cc_final: 0.7773 (tt0) REVERT: C 281 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: C 369 TYR cc_start: 0.7005 (p90) cc_final: 0.6476 (t80) REVERT: C 378 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7519 (tttp) REVERT: C 452 LEU cc_start: 0.8534 (mp) cc_final: 0.8049 (mm) REVERT: C 506 GLN cc_start: 0.7521 (mt0) cc_final: 0.6952 (mp10) REVERT: C 529 LYS cc_start: 0.8482 (mttt) cc_final: 0.7958 (tppt) REVERT: C 916 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8626 (tt) REVERT: C 994 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: C 1017 GLU cc_start: 0.8289 (tt0) cc_final: 0.8034 (tt0) outliers start: 41 outliers final: 20 residues processed: 231 average time/residue: 0.5300 time to fit residues: 144.4151 Evaluate side-chains 212 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 23 optimal weight: 0.0670 chunk 286 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 170 optimal weight: 0.0470 chunk 209 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 613 GLN A1010 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.197024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136318 restraints weight = 28164.590| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.58 r_work: 0.3362 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24435 Z= 0.093 Angle : 0.510 13.236 33312 Z= 0.261 Chirality : 0.044 0.255 3876 Planarity : 0.003 0.043 4251 Dihedral : 5.568 117.703 3832 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 1.22 % Allowed : 12.81 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2955 helix: 2.54 (0.21), residues: 668 sheet: 0.44 (0.20), residues: 657 loop : -0.29 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.019 0.001 TYR C1067 PHE 0.033 0.001 PHE B 453 TRP 0.019 0.001 TRP B 64 HIS 0.004 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00201 (24366) covalent geometry : angle 0.49753 (33144) SS BOND : bond 0.00399 ( 39) SS BOND : angle 1.26765 ( 78) hydrogen bonds : bond 0.03370 ( 1045) hydrogen bonds : angle 5.16446 ( 2880) link_NAG-ASN : bond 0.00211 ( 30) link_NAG-ASN : angle 1.96626 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.5931 (mm) REVERT: A 135 PHE cc_start: 0.6010 (t80) cc_final: 0.5616 (t80) REVERT: A 278 LYS cc_start: 0.8786 (tttt) cc_final: 0.8338 (ttmm) REVERT: A 281 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8106 (pp20) REVERT: A 347 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4017 (t80) REVERT: A 400 PHE cc_start: 0.6543 (p90) cc_final: 0.5805 (p90) REVERT: A 567 ARG cc_start: 0.7255 (mtt90) cc_final: 0.6966 (mtt90) REVERT: A 569 ILE cc_start: 0.7836 (mm) cc_final: 0.7533 (mm) REVERT: A 586 ASP cc_start: 0.6784 (t70) cc_final: 0.5774 (m-30) REVERT: A 731 MET cc_start: 0.9371 (ptt) cc_final: 0.9097 (ptt) REVERT: A 935 GLN cc_start: 0.8082 (tt0) cc_final: 0.7697 (tt0) REVERT: A 1092 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 32 PHE cc_start: 0.6475 (m-80) cc_final: 0.6164 (m-10) REVERT: B 271 GLN cc_start: 0.7995 (mt0) cc_final: 0.7639 (mt0) REVERT: B 900 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8665 (mtm) REVERT: B 916 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8813 (tp) REVERT: B 988 GLU cc_start: 0.7515 (mp0) cc_final: 0.7031 (mp0) REVERT: B 1118 ASP cc_start: 0.8573 (m-30) cc_final: 0.8344 (m-30) REVERT: C 81 ASN cc_start: 0.7943 (p0) cc_final: 0.6963 (p0) REVERT: C 200 TYR cc_start: 0.7928 (m-80) cc_final: 0.7570 (m-80) REVERT: C 237 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7729 (mtm180) REVERT: C 239 GLN cc_start: 0.8035 (tt0) cc_final: 0.7717 (tt0) REVERT: C 369 TYR cc_start: 0.7019 (p90) cc_final: 0.6451 (t80) REVERT: C 378 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7469 (tttp) REVERT: C 403 ARG cc_start: 0.6848 (ttp80) cc_final: 0.6596 (ttp80) REVERT: C 452 LEU cc_start: 0.8556 (mp) cc_final: 0.8065 (mm) REVERT: C 506 GLN cc_start: 0.7494 (mt0) cc_final: 0.7047 (mp10) REVERT: C 529 LYS cc_start: 0.8467 (mttt) cc_final: 0.7934 (tppt) REVERT: C 916 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 994 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: C 1017 GLU cc_start: 0.8279 (tt0) cc_final: 0.8070 (tt0) outliers start: 32 outliers final: 18 residues processed: 217 average time/residue: 0.5707 time to fit residues: 144.4469 Evaluate side-chains 210 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.191890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129453 restraints weight = 28031.602| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.58 r_work: 0.3284 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24435 Z= 0.218 Angle : 0.613 13.165 33312 Z= 0.316 Chirality : 0.048 0.269 3876 Planarity : 0.004 0.053 4251 Dihedral : 5.886 113.445 3832 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 1.26 % Allowed : 13.04 % Favored : 85.70 % 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: 0.43 (0.15), residues: 2955 helix: 2.03 (0.21), residues: 668 sheet: 0.24 (0.19), residues: 664 loop : -0.41 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 408 TYR 0.023 0.002 TYR A 396 PHE 0.033 0.002 PHE B 453 TRP 0.024 0.002 TRP B 64 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00533 (24366) covalent geometry : angle 0.59871 (33144) SS BOND : bond 0.00490 ( 39) SS BOND : angle 1.58510 ( 78) hydrogen bonds : bond 0.04889 ( 1045) hydrogen bonds : angle 5.55956 ( 2880) link_NAG-ASN : bond 0.00323 ( 30) link_NAG-ASN : angle 2.25780 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5969 (t80) cc_final: 0.5616 (t80) REVERT: A 281 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8276 (pp20) REVERT: A 347 PHE cc_start: 0.4816 (OUTLIER) cc_final: 0.4081 (t80) REVERT: A 400 PHE cc_start: 0.6503 (p90) cc_final: 0.5813 (p90) REVERT: A 569 ILE cc_start: 0.7958 (mm) cc_final: 0.7654 (mm) REVERT: A 586 ASP cc_start: 0.6775 (t70) cc_final: 0.5741 (m-30) REVERT: A 731 MET cc_start: 0.9338 (ptt) cc_final: 0.9129 (ptt) REVERT: B 32 PHE cc_start: 0.6520 (m-80) cc_final: 0.6242 (m-10) REVERT: B 271 GLN cc_start: 0.8039 (mt0) cc_final: 0.7699 (mt0) REVERT: B 900 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8615 (mtm) REVERT: B 988 GLU cc_start: 0.7524 (mp0) cc_final: 0.7031 (mp0) REVERT: C 200 TYR cc_start: 0.7959 (m-80) cc_final: 0.7604 (m-80) REVERT: C 237 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7716 (mtm180) REVERT: C 281 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: C 369 TYR cc_start: 0.7107 (p90) cc_final: 0.6496 (t80) REVERT: C 378 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7623 (tttp) REVERT: C 403 ARG cc_start: 0.6999 (ttp80) cc_final: 0.6647 (ttp80) REVERT: C 506 GLN cc_start: 0.7528 (mt0) cc_final: 0.6956 (mp10) REVERT: C 529 LYS cc_start: 0.8527 (mttt) cc_final: 0.8003 (tppt) REVERT: C 916 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8797 (tt) REVERT: C 994 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: C 1017 GLU cc_start: 0.8371 (tt0) cc_final: 0.8111 (tt0) outliers start: 33 outliers final: 21 residues processed: 208 average time/residue: 0.5174 time to fit residues: 127.4202 Evaluate side-chains 195 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A1010 GLN B 196 ASN C 196 ASN C 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.193284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130709 restraints weight = 27834.633| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.52 r_work: 0.3311 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24435 Z= 0.149 Angle : 0.557 12.940 33312 Z= 0.287 Chirality : 0.046 0.259 3876 Planarity : 0.004 0.043 4251 Dihedral : 5.875 119.038 3832 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.33 % Allowed : 13.23 % Favored : 85.43 % 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: 0.49 (0.15), residues: 2955 helix: 2.17 (0.21), residues: 668 sheet: 0.29 (0.20), residues: 646 loop : -0.42 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 355 TYR 0.037 0.001 TYR A 396 PHE 0.034 0.001 PHE B 453 TRP 0.020 0.001 TRP B 64 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00356 (24366) covalent geometry : angle 0.54299 (33144) SS BOND : bond 0.00429 ( 39) SS BOND : angle 1.41196 ( 78) hydrogen bonds : bond 0.04241 ( 1045) hydrogen bonds : angle 5.44981 ( 2880) link_NAG-ASN : bond 0.00213 ( 30) link_NAG-ASN : angle 2.17275 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.39 seconds wall clock time: 162 minutes 30.20 seconds (9750.20 seconds total)