Starting phenix.real_space_refine on Sat Jul 4 22:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwl_23549/07_2026/7lwl_23549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwl_23549/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lwl_23549/07_2026/7lwl_23549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwl_23549/07_2026/7lwl_23549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwl_23549/07_2026/7lwl_23549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwl_23549/07_2026/7lwl_23549.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwl_23549/07_2026/7lwl_23549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwl_23549/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 chiralities: 10 Time building chain proxies: 5.74, per 1000 atoms: 0.24 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: 1.78 Conformation dependent library (CDL) restraints added in 880.8 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: 0.87 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: 6.61 Time building geometry restraints manager: 2.45 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: 13304 17.51 - 35.03: 753 35.03 - 52.54: 133 52.54 - 70.06: 56 70.06 - 87.57: 31 Dihedral angle restraints: 14277 sinusoidal: 5550 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 14274 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: 0.04 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.540 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 13.068 87.572 8538 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/Z covalent geometry : bond 0.01331 / 0.77 (24366) covalent geometry : angle 1.79243 / 1.21 (33144) SS BOND : bond 0.01343 / 0.82 ( 39) SS BOND : angle 2.35263 / 1.54 ( 78) hydrogen bonds : bond 0.16465 / 10.80 ( 1045) hydrogen bonds : angle 8.18257 / 5.65 ( 2880) link_NAG-ASN : bond 0.01174 / 0.71 ( 30) link_NAG-ASN : angle 4.46897 / 3.01 ( 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 : 1.013 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: 0.5887 time to fit residues: 259.2216 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 : 0.814 ------------------------------------------------------------------------------- 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... A 66 HIS A 314 GLN A 519 HIS A 613 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.192862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125577 restraints weight = 28026.005| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.37 r_work: 0.3229 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: 0.8422 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24435 Z= 0.143 Angle : 0.674 13.460 33312 Z= 0.351 Chirality : 0.047 0.195 3876 Planarity : 0.004 0.040 4251 Dihedral : 5.874 40.582 3208 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Rotamer: Outliers : 2.14 % Allowed : 7.06 % 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: 0.28 (0.15), residues: 2955 helix: 1.31 (0.20), residues: 681 sheet: 0.36 (0.19), residues: 654 loop : -0.32 (0.15), residues: 1620 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/Z covalent geometry : bond 0.00305 / 0.14 (24366) covalent geometry : angle 0.64636 / 0.34 (33144) SS BOND : bond 0.00496 / 0.31 ( 39) SS BOND : angle 1.58332 / 1.04 ( 78) hydrogen bonds : bond 0.04970 / 3.31 ( 1045) hydrogen bonds : angle 6.21033 / 4.29 ( 2880) link_NAG-ASN : bond 0.00325 / 0.24 ( 30) link_NAG-ASN : angle 3.50017 / 2.38 ( 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 297 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6251 (mttm) cc_final: 0.5895 (mppt) REVERT: A 278 LYS cc_start: 0.8738 (tttt) cc_final: 0.8466 (ttmm) REVERT: A 281 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8048 (pp20) REVERT: A 347 PHE cc_start: 0.4762 (OUTLIER) cc_final: 0.4043 (t80) REVERT: A 355 ARG cc_start: 0.7599 (ttt180) cc_final: 0.7216 (tpp80) REVERT: A 568 ASP cc_start: 0.7449 (m-30) cc_final: 0.7177 (m-30) REVERT: A 569 ILE cc_start: 0.7553 (mm) cc_final: 0.7270 (mm) REVERT: A 586 ASP cc_start: 0.6804 (t70) cc_final: 0.5702 (m-30) REVERT: A 731 MET cc_start: 0.9402 (ptt) cc_final: 0.9083 (ptt) REVERT: A 964 LYS cc_start: 0.8711 (mttt) cc_final: 0.8396 (mtpt) REVERT: A 1029 MET cc_start: 0.9293 (tpp) cc_final: 0.8732 (tpp) REVERT: B 32 PHE cc_start: 0.6650 (m-80) cc_final: 0.6326 (m-10) REVERT: B 271 GLN cc_start: 0.7942 (mt0) cc_final: 0.7669 (mm-40) REVERT: B 323 THR cc_start: 0.8144 (m) cc_final: 0.7574 (p) REVERT: B 334 ASN cc_start: 0.6319 (m-40) cc_final: 0.5787 (p0) REVERT: B 359 SER cc_start: 0.8831 (p) cc_final: 0.8396 (m) REVERT: B 935 GLN cc_start: 0.7925 (mt0) cc_final: 0.7586 (tt0) REVERT: B 985 ASP cc_start: 0.7613 (p0) cc_final: 0.7368 (p0) REVERT: B 988 GLU cc_start: 0.7605 (mp0) cc_final: 0.7396 (mp0) REVERT: C 81 ASN cc_start: 0.8062 (p0) cc_final: 0.7264 (p0) REVERT: C 121 ASN cc_start: 0.7430 (t0) cc_final: 0.7067 (m-40) REVERT: C 170 TYR cc_start: 0.7824 (t80) cc_final: 0.7593 (t80) REVERT: C 188 ASN cc_start: 0.5839 (m110) cc_final: 0.5145 (p0) REVERT: C 200 TYR cc_start: 0.7976 (m-80) cc_final: 0.7613 (m-80) REVERT: C 205 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8704 (t) REVERT: C 237 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7647 (mtm180) REVERT: C 369 TYR cc_start: 0.7015 (p90) cc_final: 0.6458 (t80) REVERT: C 375 SER cc_start: 0.7759 (m) cc_final: 0.7510 (p) REVERT: C 378 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7452 (tttp) REVERT: C 393 THR cc_start: 0.8084 (m) cc_final: 0.7870 (p) REVERT: C 405 ASP cc_start: 0.7430 (m-30) cc_final: 0.7184 (m-30) REVERT: C 452 LEU cc_start: 0.8201 (mp) cc_final: 0.7697 (mm) REVERT: C 505 TYR cc_start: 0.7290 (m-80) cc_final: 0.6631 (t80) REVERT: C 529 LYS cc_start: 0.8334 (mttt) cc_final: 0.7838 (tppt) REVERT: C 572 THR cc_start: 0.8730 (p) cc_final: 0.8525 (t) REVERT: C 574 ASP cc_start: 0.8423 (t70) cc_final: 0.8096 (t0) REVERT: C 776 LYS cc_start: 0.8856 (tttt) cc_final: 0.8575 (ttpp) REVERT: C 804 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: C 1017 GLU cc_start: 0.8530 (tt0) cc_final: 0.8269 (tt0) outliers start: 56 outliers final: 21 residues processed: 281 average time/residue: 0.5038 time to fit residues: 167.8691 Evaluate side-chains 211 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 3.9990 chunk 256 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 214 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.191547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124894 restraints weight = 28094.580| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.49 r_work: 0.3199 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24435 Z= 0.138 Angle : 0.616 12.398 33312 Z= 0.315 Chirality : 0.046 0.371 3876 Planarity : 0.004 0.046 4251 Dihedral : 5.302 37.166 3205 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 2.06 % Allowed : 9.04 % Favored : 88.90 % 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: 0.44 (0.15), residues: 2955 helix: 1.81 (0.21), residues: 674 sheet: 0.35 (0.19), residues: 637 loop : -0.34 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 403 TYR 0.022 0.001 TYR C 369 PHE 0.027 0.002 PHE B 453 TRP 0.025 0.001 TRP B 64 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (24366) covalent geometry : angle 0.59638 / 0.31 (33144) SS BOND : bond 0.00339 / 0.22 ( 39) SS BOND : angle 1.27163 / 0.83 ( 78) hydrogen bonds : bond 0.04566 / 3.06 ( 1045) hydrogen bonds : angle 5.86624 / 4.04 ( 2880) link_NAG-ASN : bond 0.00806 / 0.37 ( 30) link_NAG-ASN : angle 2.87455 / 2.05 ( 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 262 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6379 (mttm) cc_final: 0.6141 (mppt) REVERT: A 278 LYS cc_start: 0.8732 (tttt) cc_final: 0.8392 (ttmm) REVERT: A 281 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8152 (pp20) REVERT: A 355 ARG cc_start: 0.7656 (ttt180) cc_final: 0.7320 (tpp80) REVERT: A 400 PHE cc_start: 0.6388 (p90) cc_final: 0.5747 (p90) REVERT: A 569 ILE cc_start: 0.7612 (mm) cc_final: 0.7291 (mm) REVERT: A 586 ASP cc_start: 0.6969 (t70) cc_final: 0.5796 (m-30) REVERT: A 731 MET cc_start: 0.9421 (ptt) cc_final: 0.9062 (ptt) REVERT: A 1029 MET cc_start: 0.9181 (tpp) cc_final: 0.8705 (tpp) REVERT: B 32 PHE cc_start: 0.6719 (m-80) cc_final: 0.6313 (m-10) REVERT: B 271 GLN cc_start: 0.7984 (mt0) cc_final: 0.7719 (mm-40) REVERT: B 323 THR cc_start: 0.8119 (m) cc_final: 0.7634 (p) REVERT: B 811 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6716 (mppt) REVERT: B 900 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8647 (mtm) REVERT: B 916 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8850 (tt) REVERT: B 935 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: B 985 ASP cc_start: 0.7633 (p0) cc_final: 0.7431 (p0) REVERT: B 988 GLU cc_start: 0.7506 (mp0) cc_final: 0.7227 (mp0) REVERT: C 81 ASN cc_start: 0.8051 (p0) cc_final: 0.7069 (p0) REVERT: C 121 ASN cc_start: 0.7358 (t0) cc_final: 0.7017 (m-40) REVERT: C 170 TYR cc_start: 0.7896 (t80) cc_final: 0.7682 (t80) REVERT: C 188 ASN cc_start: 0.5934 (m110) cc_final: 0.5256 (p0) REVERT: C 200 TYR cc_start: 0.7923 (m-80) cc_final: 0.7507 (m-80) REVERT: C 237 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7682 (mtm180) REVERT: C 239 GLN cc_start: 0.8165 (tt0) cc_final: 0.7916 (tt0) REVERT: C 281 GLU cc_start: 0.8796 (pt0) cc_final: 0.8578 (pm20) REVERT: C 369 TYR cc_start: 0.6942 (p90) cc_final: 0.6453 (t80) REVERT: C 378 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7409 (tttp) REVERT: C 393 THR cc_start: 0.8326 (m) cc_final: 0.8063 (p) REVERT: C 405 ASP cc_start: 0.7321 (m-30) cc_final: 0.7004 (m-30) REVERT: C 452 LEU cc_start: 0.8146 (mp) cc_final: 0.7695 (mm) REVERT: C 453 PHE cc_start: 0.7635 (p90) cc_final: 0.7255 (p90) REVERT: C 505 TYR cc_start: 0.7398 (m-80) cc_final: 0.6734 (t80) REVERT: C 506 GLN cc_start: 0.7380 (mt0) cc_final: 0.7168 (mt0) REVERT: C 529 LYS cc_start: 0.8400 (mttt) cc_final: 0.7859 (tppt) REVERT: C 572 THR cc_start: 0.8773 (p) cc_final: 0.8547 (t) REVERT: C 574 ASP cc_start: 0.8424 (t70) cc_final: 0.8165 (t0) REVERT: C 994 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: C 1017 GLU cc_start: 0.8610 (tt0) cc_final: 0.8375 (tt0) REVERT: C 1145 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6635 (mp) outliers start: 54 outliers final: 27 residues processed: 247 average time/residue: 0.4764 time to fit residues: 140.7884 Evaluate side-chains 218 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 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 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 987 VAL Chi-restraints excluded: chain B residue 1081 ILE 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 Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 204 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 299 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4250 r_free = 0.4250 target = 0.195972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134581 restraints weight = 28284.074| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.56 r_work: 0.3344 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24435 Z= 0.107 Angle : 0.544 8.596 33312 Z= 0.280 Chirality : 0.045 0.194 3876 Planarity : 0.003 0.048 4251 Dihedral : 4.776 25.377 3205 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 1.91 % Allowed : 9.69 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 2955 helix: 2.11 (0.21), residues: 674 sheet: 0.31 (0.19), residues: 634 loop : -0.31 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.019 0.001 TYR C1067 PHE 0.030 0.001 PHE B 453 TRP 0.024 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (24366) covalent geometry : angle 0.52758 / 0.28 (33144) SS BOND : bond 0.00471 / 0.31 ( 39) SS BOND : angle 1.36309 / 0.90 ( 78) hydrogen bonds : bond 0.03859 / 2.58 ( 1045) hydrogen bonds : angle 5.56101 / 3.82 ( 2880) link_NAG-ASN : bond 0.00353 / 0.18 ( 30) link_NAG-ASN : angle 2.33327 / 1.69 ( 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 255 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3659 (mt) REVERT: A 129 LYS cc_start: 0.6500 (mttm) cc_final: 0.6226 (mppt) REVERT: A 278 LYS cc_start: 0.8811 (tttt) cc_final: 0.8463 (ttmm) REVERT: A 281 GLU cc_start: 0.8415 (pp20) cc_final: 0.8133 (pp20) REVERT: A 347 PHE cc_start: 0.4489 (OUTLIER) cc_final: 0.4273 (t80) REVERT: A 355 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7507 (tpp80) REVERT: A 400 PHE cc_start: 0.6559 (p90) cc_final: 0.5966 (p90) REVERT: A 569 ILE cc_start: 0.7634 (mm) cc_final: 0.7249 (mm) REVERT: A 586 ASP cc_start: 0.6874 (t70) cc_final: 0.5858 (m-30) REVERT: A 731 MET cc_start: 0.9352 (ptt) cc_final: 0.9073 (ptt) REVERT: A 1029 MET cc_start: 0.8985 (tpp) cc_final: 0.8534 (tpp) REVERT: B 32 PHE cc_start: 0.6813 (m-80) cc_final: 0.6423 (m-10) REVERT: B 271 GLN cc_start: 0.7971 (mt0) cc_final: 0.7710 (mm-40) REVERT: B 323 THR cc_start: 0.8247 (m) cc_final: 0.7860 (p) REVERT: B 619 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: B 854 LYS cc_start: 0.5436 (mttm) cc_final: 0.5221 (mttm) REVERT: B 900 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: B 916 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8849 (tp) REVERT: B 957 GLN cc_start: 0.8555 (tt0) cc_final: 0.8339 (tt0) REVERT: B 988 GLU cc_start: 0.7498 (mp0) cc_final: 0.7255 (mp0) REVERT: C 81 ASN cc_start: 0.8034 (p0) cc_final: 0.7101 (p0) REVERT: C 121 ASN cc_start: 0.7404 (t0) cc_final: 0.7139 (m-40) REVERT: C 170 TYR cc_start: 0.7890 (t80) cc_final: 0.7660 (t80) REVERT: C 188 ASN cc_start: 0.6153 (m110) cc_final: 0.5476 (p0) REVERT: C 200 TYR cc_start: 0.7978 (m-80) cc_final: 0.7630 (m-80) REVERT: C 237 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7829 (mtm180) REVERT: C 239 GLN cc_start: 0.8142 (tt0) cc_final: 0.7911 (tt0) REVERT: C 369 TYR cc_start: 0.6947 (p90) cc_final: 0.6481 (t80) REVERT: C 378 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7418 (tttp) REVERT: C 405 ASP cc_start: 0.7260 (m-30) cc_final: 0.7042 (m-30) REVERT: C 452 LEU cc_start: 0.8307 (mp) cc_final: 0.7925 (mm) REVERT: C 453 PHE cc_start: 0.7820 (p90) cc_final: 0.7502 (p90) REVERT: C 505 TYR cc_start: 0.7449 (m-80) cc_final: 0.6748 (t80) REVERT: C 506 GLN cc_start: 0.7657 (mt0) cc_final: 0.7440 (mt0) REVERT: C 529 LYS cc_start: 0.8390 (mttt) cc_final: 0.7932 (tppt) REVERT: C 581 THR cc_start: 0.8952 (m) cc_final: 0.8701 (p) REVERT: C 957 GLN cc_start: 0.8653 (tt0) cc_final: 0.8449 (tt0) REVERT: C 994 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: C 1017 GLU cc_start: 0.8372 (tt0) cc_final: 0.8140 (tt0) outliers start: 50 outliers final: 19 residues processed: 243 average time/residue: 0.5353 time to fit residues: 154.1590 Evaluate side-chains 215 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 878 LEU Chi-restraints excluded: chain A residue 886 TRP 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 196 ASN 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 619 GLU 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 C residue 33 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 385 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 878 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 157 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 296 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 354 ASN A 901 GLN B 196 ASN B 901 GLN B 935 GLN C 196 ASN C 207 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.194781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134838 restraints weight = 28114.884| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.48 r_work: 0.3329 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24435 Z= 0.128 Angle : 0.551 9.265 33312 Z= 0.283 Chirality : 0.045 0.240 3876 Planarity : 0.003 0.048 4251 Dihedral : 4.671 25.247 3204 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 2.06 % Allowed : 10.49 % Favored : 87.45 % 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: 0.57 (0.15), residues: 2955 helix: 2.12 (0.21), residues: 674 sheet: 0.37 (0.19), residues: 640 loop : -0.34 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.019 0.001 TYR C1067 PHE 0.029 0.001 PHE B 453 TRP 0.021 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24366) covalent geometry : angle 0.53637 / 0.28 (33144) SS BOND : bond 0.00313 / 0.19 ( 39) SS BOND : angle 1.39719 / 0.91 ( 78) hydrogen bonds : bond 0.04088 / 2.74 ( 1045) hydrogen bonds : angle 5.51417 / 3.78 ( 2880) link_NAG-ASN : bond 0.00234 / 0.15 ( 30) link_NAG-ASN : angle 2.14312 / 1.49 ( 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 253 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6486 (mttm) cc_final: 0.6133 (mppt) REVERT: A 135 PHE cc_start: 0.6316 (t80) cc_final: 0.5869 (t80) REVERT: A 278 LYS cc_start: 0.8765 (tttt) cc_final: 0.8395 (ttmm) REVERT: A 281 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8098 (pp20) REVERT: A 347 PHE cc_start: 0.4639 (OUTLIER) cc_final: 0.4379 (t80) REVERT: A 355 ARG cc_start: 0.7825 (ttt180) cc_final: 0.7550 (tpp80) REVERT: A 400 PHE cc_start: 0.6465 (p90) cc_final: 0.5930 (p90) REVERT: A 569 ILE cc_start: 0.7777 (mm) cc_final: 0.7462 (mm) REVERT: A 586 ASP cc_start: 0.6927 (t70) cc_final: 0.5918 (m-30) REVERT: A 603 ASN cc_start: 0.6914 (t0) cc_final: 0.6569 (t0) REVERT: A 731 MET cc_start: 0.9379 (ptt) cc_final: 0.9113 (ptt) REVERT: A 1029 MET cc_start: 0.9058 (tpp) cc_final: 0.8610 (tpp) REVERT: B 32 PHE cc_start: 0.6715 (m-80) cc_final: 0.6391 (m-10) REVERT: B 271 GLN cc_start: 0.7939 (mt0) cc_final: 0.7655 (mm-40) REVERT: B 323 THR cc_start: 0.8332 (m) cc_final: 0.7968 (p) REVERT: B 740 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: B 900 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: B 916 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8834 (tp) REVERT: B 957 GLN cc_start: 0.8472 (tt0) cc_final: 0.8265 (tt0) REVERT: B 988 GLU cc_start: 0.7398 (mp0) cc_final: 0.6882 (mp0) REVERT: C 81 ASN cc_start: 0.7882 (p0) cc_final: 0.6935 (p0) REVERT: C 121 ASN cc_start: 0.7364 (t0) cc_final: 0.7095 (m-40) REVERT: C 188 ASN cc_start: 0.5849 (m110) cc_final: 0.5161 (p0) REVERT: C 200 TYR cc_start: 0.7964 (m-80) cc_final: 0.7574 (m-80) REVERT: C 237 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7773 (mtm180) REVERT: C 239 GLN cc_start: 0.8097 (tt0) cc_final: 0.7835 (tt0) REVERT: C 269 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: C 281 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: C 369 TYR cc_start: 0.6921 (p90) cc_final: 0.6453 (t80) REVERT: C 378 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7406 (tttp) REVERT: C 453 PHE cc_start: 0.7722 (p90) cc_final: 0.7404 (p90) REVERT: C 505 TYR cc_start: 0.7454 (m-80) cc_final: 0.6854 (t80) REVERT: C 506 GLN cc_start: 0.7755 (mt0) cc_final: 0.7526 (mt0) REVERT: C 529 LYS cc_start: 0.8420 (mttt) cc_final: 0.7950 (tppt) REVERT: C 583 GLU cc_start: 0.8381 (pt0) cc_final: 0.7814 (pt0) REVERT: C 916 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8738 (tt) REVERT: C 994 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: C 1017 GLU cc_start: 0.8359 (tt0) cc_final: 0.8120 (tt0) outliers start: 54 outliers final: 26 residues processed: 239 average time/residue: 0.5204 time to fit residues: 148.1699 Evaluate side-chains 224 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 604 THR 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 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 196 ASN 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 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 982 SER 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 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 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 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 170 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 354 ASN B 196 ASN B 580 GLN B 914 ASN B1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.190067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127432 restraints weight = 27986.959| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.50 r_work: 0.3253 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 24435 Z= 0.293 Angle : 0.685 11.084 33312 Z= 0.352 Chirality : 0.051 0.269 3876 Planarity : 0.004 0.051 4251 Dihedral : 5.261 40.004 3204 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 2.63 % Allowed : 11.02 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 2955 helix: 1.65 (0.21), residues: 661 sheet: 0.14 (0.19), residues: 647 loop : -0.54 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 905 TYR 0.024 0.002 TYR A 91 PHE 0.031 0.002 PHE B 453 TRP 0.018 0.002 TRP B 64 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.29 (24366) covalent geometry : angle 0.67012 / 0.35 (33144) SS BOND : bond 0.00484 / 0.31 ( 39) SS BOND : angle 1.65663 / 1.08 ( 78) hydrogen bonds : bond 0.05647 / 3.78 ( 1045) hydrogen bonds : angle 5.94349 / 4.08 ( 2880) link_NAG-ASN : bond 0.00357 / 0.26 ( 30) link_NAG-ASN : angle 2.46964 / 1.66 ( 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 265 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6094 (t80) cc_final: 0.5767 (t80) REVERT: A 202 LYS cc_start: 0.6002 (mttt) cc_final: 0.5373 (mtpt) REVERT: A 218 GLN cc_start: 0.8065 (tp40) cc_final: 0.7814 (tp40) REVERT: A 281 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: A 355 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7642 (tpp80) REVERT: A 400 PHE cc_start: 0.6444 (p90) cc_final: 0.6009 (p90) REVERT: A 569 ILE cc_start: 0.8023 (mm) cc_final: 0.7747 (mm) REVERT: A 586 ASP cc_start: 0.6830 (t70) cc_final: 0.5782 (m-30) REVERT: A 603 ASN cc_start: 0.7425 (t0) cc_final: 0.6982 (t0) REVERT: A 619 GLU cc_start: 0.7767 (mp0) cc_final: 0.7563 (mp0) REVERT: A 731 MET cc_start: 0.9316 (ptt) cc_final: 0.9098 (ptt) REVERT: A 740 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8122 (tpt) REVERT: A 1029 MET cc_start: 0.9217 (tpp) cc_final: 0.8832 (tpp) REVERT: B 32 PHE cc_start: 0.6643 (m-80) cc_final: 0.6342 (m-10) REVERT: B 271 GLN cc_start: 0.8058 (mt0) cc_final: 0.7832 (mm-40) REVERT: B 323 THR cc_start: 0.8288 (m) cc_final: 0.8022 (p) REVERT: B 400 PHE cc_start: 0.8421 (p90) cc_final: 0.8199 (p90) REVERT: B 564 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: B 740 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8347 (ttt) REVERT: B 988 GLU cc_start: 0.7541 (mp0) cc_final: 0.7232 (mp0) REVERT: C 81 ASN cc_start: 0.7909 (p0) cc_final: 0.6948 (p0) REVERT: C 121 ASN cc_start: 0.7432 (t0) cc_final: 0.7157 (m-40) REVERT: C 200 TYR cc_start: 0.8071 (m-80) cc_final: 0.7808 (m-80) REVERT: C 237 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7904 (mtm180) REVERT: C 239 GLN cc_start: 0.8264 (tt0) cc_final: 0.7979 (tt0) REVERT: C 269 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: C 281 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: C 319 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: C 369 TYR cc_start: 0.7040 (p90) cc_final: 0.6455 (t80) REVERT: C 378 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7553 (tttp) REVERT: C 505 TYR cc_start: 0.7443 (m-80) cc_final: 0.6762 (t80) REVERT: C 529 LYS cc_start: 0.8495 (mttt) cc_final: 0.8077 (tppt) REVERT: C 916 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8877 (tt) REVERT: C 994 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: C 1017 GLU cc_start: 0.8392 (tt0) cc_final: 0.8150 (tt0) outliers start: 69 outliers final: 32 residues processed: 243 average time/residue: 0.5435 time to fit residues: 156.0156 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 : 0.854 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 740 MET 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 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 564 GLN 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 319 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 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 1104 VAL 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: 0.0570 chunk 209 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN A 354 ASN B 196 ASN C 196 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.191127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129267 restraints weight = 27915.556| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.62 r_work: 0.3280 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24435 Z= 0.216 Angle : 0.625 11.737 33312 Z= 0.319 Chirality : 0.048 0.266 3876 Planarity : 0.004 0.045 4251 Dihedral : 5.094 44.506 3204 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 12.01 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.15), residues: 2955 helix: 1.77 (0.21), residues: 662 sheet: 0.24 (0.20), residues: 631 loop : -0.60 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 403 TYR 0.022 0.002 TYR A 91 PHE 0.033 0.002 PHE B 453 TRP 0.016 0.002 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (24366) covalent geometry : angle 0.60592 / 0.31 (33144) SS BOND : bond 0.00461 / 0.30 ( 39) SS BOND : angle 1.52898 / 1.00 ( 78) hydrogen bonds : bond 0.04925 / 3.30 ( 1045) hydrogen bonds : angle 5.78920 / 3.97 ( 2880) link_NAG-ASN : bond 0.00479 / 0.23 ( 30) link_NAG-ASN : angle 2.74528 / 1.76 ( 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 249 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6109 (t80) cc_final: 0.5745 (t80) REVERT: A 281 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8332 (pp20) REVERT: A 355 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7629 (tpp80) REVERT: A 400 PHE cc_start: 0.6384 (p90) cc_final: 0.6048 (p90) REVERT: A 569 ILE cc_start: 0.7975 (mm) cc_final: 0.7667 (mm) REVERT: A 586 ASP cc_start: 0.6904 (t70) cc_final: 0.5865 (m-30) REVERT: A 603 ASN cc_start: 0.7293 (t0) cc_final: 0.6855 (t0) REVERT: A 731 MET cc_start: 0.9340 (ptt) cc_final: 0.9068 (ptt) REVERT: A 1029 MET cc_start: 0.9202 (tpp) cc_final: 0.8847 (tpp) REVERT: A 1144 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 32 PHE cc_start: 0.6540 (m-80) cc_final: 0.6224 (m-10) REVERT: B 271 GLN cc_start: 0.8009 (mt0) cc_final: 0.7751 (mm-40) REVERT: B 323 THR cc_start: 0.8373 (m) cc_final: 0.8145 (p) REVERT: B 564 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: B 740 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8277 (ttt) REVERT: C 81 ASN cc_start: 0.7905 (p0) cc_final: 0.6942 (p0) REVERT: C 121 ASN cc_start: 0.7297 (t0) cc_final: 0.7057 (m-40) REVERT: C 200 TYR cc_start: 0.8086 (m-80) cc_final: 0.7715 (m-80) REVERT: C 237 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7813 (mtm180) REVERT: C 239 GLN cc_start: 0.8173 (tt0) cc_final: 0.7860 (tt0) REVERT: C 269 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: C 281 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: C 369 TYR cc_start: 0.7032 (p90) cc_final: 0.6443 (t80) REVERT: C 378 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7434 (tttp) REVERT: C 505 TYR cc_start: 0.7542 (m-80) cc_final: 0.6851 (t80) REVERT: C 529 LYS cc_start: 0.8490 (mttt) cc_final: 0.8038 (tppt) REVERT: C 916 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8819 (tt) REVERT: C 994 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: C 1017 GLU cc_start: 0.8395 (tt0) cc_final: 0.8111 (tt0) outliers start: 54 outliers final: 33 residues processed: 232 average time/residue: 0.5066 time to fit residues: 140.1935 Evaluate side-chains 227 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain A residue 604 THR 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 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 564 GLN 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 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 66 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 276 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN B 196 ASN 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 = 0.4224 r_free = 0.4224 target = 0.193208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130623 restraints weight = 27981.303| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.52 r_work: 0.3299 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24435 Z= 0.129 Angle : 0.574 12.172 33312 Z= 0.292 Chirality : 0.046 0.260 3876 Planarity : 0.004 0.044 4251 Dihedral : 4.858 40.606 3204 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 2.21 % Allowed : 12.43 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 2955 helix: 2.12 (0.21), residues: 662 sheet: 0.28 (0.20), residues: 624 loop : -0.55 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.024 0.001 TYR C 170 PHE 0.062 0.001 PHE A 347 TRP 0.015 0.001 TRP B 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24366) covalent geometry : angle 0.55382 / 0.29 (33144) SS BOND : bond 0.00420 / 0.27 ( 39) SS BOND : angle 1.69143 / 1.10 ( 78) hydrogen bonds : bond 0.04191 / 2.81 ( 1045) hydrogen bonds : angle 5.57251 / 3.80 ( 2880) link_NAG-ASN : bond 0.00381 / 0.19 ( 30) link_NAG-ASN : angle 2.55920 / 1.63 ( 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 252 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6078 (t80) cc_final: 0.5722 (t80) REVERT: A 281 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8340 (pp20) REVERT: A 347 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4518 (t80) REVERT: A 355 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7587 (tpp80) REVERT: A 400 PHE cc_start: 0.6381 (p90) cc_final: 0.6029 (p90) REVERT: A 569 ILE cc_start: 0.7874 (mm) cc_final: 0.7559 (mm) REVERT: A 586 ASP cc_start: 0.6843 (t70) cc_final: 0.5845 (m-30) REVERT: A 603 ASN cc_start: 0.7158 (t0) cc_final: 0.6762 (t0) REVERT: A 619 GLU cc_start: 0.7335 (mp0) cc_final: 0.7049 (mp0) REVERT: A 731 MET cc_start: 0.9334 (ptt) cc_final: 0.9077 (ptt) REVERT: A 1029 MET cc_start: 0.9086 (tpp) cc_final: 0.8851 (tpp) REVERT: B 32 PHE cc_start: 0.6544 (m-80) cc_final: 0.6230 (m-10) REVERT: B 271 GLN cc_start: 0.8070 (mt0) cc_final: 0.7747 (mt0) REVERT: B 564 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: B 988 GLU cc_start: 0.7476 (mp0) cc_final: 0.7128 (mp0) REVERT: C 81 ASN cc_start: 0.7935 (p0) cc_final: 0.6969 (p0) REVERT: C 140 PHE cc_start: 0.7980 (p90) cc_final: 0.7729 (t80) REVERT: C 200 TYR cc_start: 0.8088 (m-80) cc_final: 0.7702 (m-80) REVERT: C 237 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7838 (mtm180) REVERT: C 239 GLN cc_start: 0.8173 (tt0) cc_final: 0.7939 (tt0) REVERT: C 369 TYR cc_start: 0.7086 (p90) cc_final: 0.6431 (t80) REVERT: C 378 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7702 (tttp) REVERT: C 529 LYS cc_start: 0.8501 (mttt) cc_final: 0.8057 (tppt) REVERT: C 916 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8727 (tt) REVERT: C 994 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: C 1017 GLU cc_start: 0.8387 (tt0) cc_final: 0.8129 (tt0) outliers start: 58 outliers final: 25 residues processed: 240 average time/residue: 0.5275 time to fit residues: 150.8539 Evaluate side-chains 215 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 604 THR 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 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 564 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 982 SER 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 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 Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 23 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 294 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 354 ASN A 613 GLN B 196 ASN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.193858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131625 restraints weight = 27977.481| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.48 r_work: 0.3324 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24435 Z= 0.124 Angle : 0.554 13.201 33312 Z= 0.283 Chirality : 0.045 0.265 3876 Planarity : 0.004 0.044 4251 Dihedral : 4.672 35.615 3204 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.60 % Allowed : 13.12 % Favored : 85.28 % 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: 0.45 (0.15), residues: 2955 helix: 2.22 (0.21), residues: 668 sheet: 0.31 (0.20), residues: 637 loop : -0.51 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.019 0.001 TYR C1067 PHE 0.033 0.001 PHE B 453 TRP 0.013 0.001 TRP B 64 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (24366) covalent geometry : angle 0.53710 / 0.28 (33144) SS BOND : bond 0.00442 / 0.28 ( 39) SS BOND : angle 1.42985 / 0.94 ( 78) hydrogen bonds : bond 0.03995 / 2.68 ( 1045) hydrogen bonds : angle 5.44052 / 3.71 ( 2880) link_NAG-ASN : bond 0.00366 / 0.16 ( 30) link_NAG-ASN : angle 2.39184 / 1.51 ( 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 233 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6060 (t80) cc_final: 0.5702 (t80) REVERT: A 281 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8217 (pp20) REVERT: A 347 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.4455 (t80) REVERT: A 355 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7590 (tpp80) REVERT: A 400 PHE cc_start: 0.6512 (p90) cc_final: 0.6088 (p90) REVERT: A 569 ILE cc_start: 0.7880 (mm) cc_final: 0.7583 (mm) REVERT: A 586 ASP cc_start: 0.6799 (t70) cc_final: 0.5800 (m-30) REVERT: A 603 ASN cc_start: 0.6893 (t0) cc_final: 0.6508 (t0) REVERT: A 619 GLU cc_start: 0.7012 (mp0) cc_final: 0.6690 (mp0) REVERT: A 731 MET cc_start: 0.9360 (ptt) cc_final: 0.9113 (ptt) REVERT: A 1029 MET cc_start: 0.9071 (tpp) cc_final: 0.8636 (tpp) REVERT: B 32 PHE cc_start: 0.6479 (m-80) cc_final: 0.6211 (m-10) REVERT: B 271 GLN cc_start: 0.7989 (mt0) cc_final: 0.7617 (mt0) REVERT: B 988 GLU cc_start: 0.7449 (mp0) cc_final: 0.6952 (mp0) REVERT: B 1118 ASP cc_start: 0.8588 (m-30) cc_final: 0.8350 (m-30) REVERT: C 81 ASN cc_start: 0.7918 (p0) cc_final: 0.6953 (p0) REVERT: C 200 TYR cc_start: 0.7932 (m-80) cc_final: 0.7568 (m-80) REVERT: C 237 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7769 (mtm180) REVERT: C 239 GLN cc_start: 0.8135 (tt0) cc_final: 0.7863 (tt0) REVERT: C 369 TYR cc_start: 0.7110 (p90) cc_final: 0.6479 (t80) REVERT: C 378 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7575 (tttp) REVERT: C 403 ARG cc_start: 0.6862 (ttp80) cc_final: 0.6627 (ttp80) REVERT: C 506 GLN cc_start: 0.7630 (mt0) cc_final: 0.6960 (mp10) REVERT: C 529 LYS cc_start: 0.8522 (mttt) cc_final: 0.7988 (tppt) REVERT: C 916 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8715 (tt) REVERT: C 994 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: C 1017 GLU cc_start: 0.8366 (tt0) cc_final: 0.8119 (tt0) outliers start: 42 outliers final: 27 residues processed: 224 average time/residue: 0.5409 time to fit residues: 144.5173 Evaluate side-chains 215 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 604 THR 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 286 THR 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 854 LYS Chi-restraints excluded: chain B residue 982 SER 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 170 TYR 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 Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 132 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 354 ASN A 613 GLN B 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.191679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128353 restraints weight = 28094.299| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.55 r_work: 0.3278 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24435 Z= 0.202 Angle : 0.609 12.871 33312 Z= 0.310 Chirality : 0.048 0.266 3876 Planarity : 0.004 0.046 4251 Dihedral : 4.870 37.890 3204 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 13.20 % Favored : 85.28 % 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: 0.28 (0.15), residues: 2955 helix: 2.03 (0.21), residues: 662 sheet: 0.26 (0.20), residues: 624 loop : -0.59 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 905 TYR 0.021 0.002 TYR C 170 PHE 0.033 0.002 PHE B 453 TRP 0.021 0.002 TRP B 64 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (24366) covalent geometry : angle 0.59170 / 0.31 (33144) SS BOND : bond 0.00484 / 0.31 ( 39) SS BOND : angle 1.57403 / 1.03 ( 78) hydrogen bonds : bond 0.04707 / 3.16 ( 1045) hydrogen bonds : angle 5.59752 / 3.81 ( 2880) link_NAG-ASN : bond 0.00408 / 0.21 ( 30) link_NAG-ASN : angle 2.48926 / 1.57 ( 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 224 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6079 (t80) cc_final: 0.5731 (t80) REVERT: A 281 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: A 347 PHE cc_start: 0.5023 (OUTLIER) cc_final: 0.4525 (t80) REVERT: A 355 ARG cc_start: 0.7909 (ttt180) cc_final: 0.7702 (tpp80) REVERT: A 400 PHE cc_start: 0.6512 (p90) cc_final: 0.6098 (p90) REVERT: A 569 ILE cc_start: 0.7936 (mm) cc_final: 0.7615 (mm) REVERT: A 586 ASP cc_start: 0.6727 (t70) cc_final: 0.5805 (m-30) REVERT: A 603 ASN cc_start: 0.7098 (t0) cc_final: 0.6702 (t0) REVERT: A 619 GLU cc_start: 0.7073 (mp0) cc_final: 0.6772 (mp0) REVERT: A 731 MET cc_start: 0.9308 (ptt) cc_final: 0.9047 (ptt) REVERT: B 32 PHE cc_start: 0.6542 (m-80) cc_final: 0.6303 (m-10) REVERT: B 271 GLN cc_start: 0.8070 (mt0) cc_final: 0.7735 (mt0) REVERT: B 988 GLU cc_start: 0.7550 (mp0) cc_final: 0.7113 (mp0) REVERT: C 140 PHE cc_start: 0.7681 (t80) cc_final: 0.7410 (t80) REVERT: C 200 TYR cc_start: 0.7991 (m-80) cc_final: 0.7635 (m-80) REVERT: C 237 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7863 (mtm180) REVERT: C 369 TYR cc_start: 0.7098 (p90) cc_final: 0.6547 (t80) REVERT: C 378 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7721 (tttp) REVERT: C 506 GLN cc_start: 0.7651 (mt0) cc_final: 0.6982 (mp10) REVERT: C 529 LYS cc_start: 0.8530 (mttt) cc_final: 0.8029 (tppt) REVERT: C 916 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (tt) REVERT: C 994 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: C 1017 GLU cc_start: 0.8424 (tt0) cc_final: 0.8169 (tt0) outliers start: 40 outliers final: 29 residues processed: 217 average time/residue: 0.5604 time to fit residues: 144.3492 Evaluate side-chains 211 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 345 THR Chi-restraints excluded: chain A residue 347 PHE 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 286 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 441 LEU 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 854 LYS Chi-restraints excluded: chain B residue 982 SER 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 170 TYR 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 Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN B 196 ASN C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.191823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128864 restraints weight = 27868.894| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.48 r_work: 0.3285 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 24435 Z= 0.207 Angle : 0.812 59.200 33312 Z= 0.457 Chirality : 0.051 1.137 3876 Planarity : 0.004 0.124 4251 Dihedral : 4.872 37.894 3204 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.45 % Allowed : 13.39 % Favored : 85.16 % 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: 0.27 (0.15), residues: 2955 helix: 2.03 (0.21), residues: 662 sheet: 0.26 (0.20), residues: 624 loop : -0.61 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.252 0.002 TYR C 170 PHE 0.032 0.002 PHE B 453 TRP 0.019 0.002 TRP B 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (24366) covalent geometry : angle 0.80032 / 0.46 (33144) SS BOND : bond 0.00456 / 0.29 ( 39) SS BOND : angle 1.53179 / 1.00 ( 78) hydrogen bonds : bond 0.04632 / 3.12 ( 1045) hydrogen bonds : angle 5.59511 / 3.81 ( 2880) link_NAG-ASN : bond 0.00407 / 0.21 ( 30) link_NAG-ASN : angle 2.49090 / 1.57 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9401.80 seconds wall clock time: 160 minutes 43.09 seconds (9643.09 seconds total)