Starting phenix.real_space_refine on Fri Mar 6 16:57:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uow_26656/03_2026/7uow_26656.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uow_26656/03_2026/7uow_26656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uow_26656/03_2026/7uow_26656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uow_26656/03_2026/7uow_26656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uow_26656/03_2026/7uow_26656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uow_26656/03_2026/7uow_26656.map" } resolution = 4.4 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= -0.005 sd= 0.055 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 139 5.16 5 C 20681 2.51 5 N 5377 2.21 5 O 6369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32566 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8483 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 58, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8341 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 8516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8516 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "H" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 11, 'TRANS': 210} Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1634 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "J" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1650 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "L" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1634 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.48, per 1000 atoms: 0.20 Number of scatterers: 32566 At special positions: 0 Unit cell: (166.78, 159.296, 254.446, 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 139 16.00 O 6369 8.00 N 5377 7.00 C 20681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 343 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 709 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 331 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7672 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 71 sheets defined 21.9% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.502A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.744A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.067A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.701A 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 removed outlier: 3.530A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.686A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.640A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.801A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.679A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.507A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.621A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.582A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 3.685A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.886A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.835A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.935A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.531A 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 616 through 623 removed outlier: 3.784A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.696A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.517A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 916 through 918 No H-bonds generated for 'chain 'B' and resid 916 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.049A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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: 4.308A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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: 5.827A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 4.311A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.992A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.963A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.980A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 423 Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.711A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 3.890A pdb=" N ILE C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 624' Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.771A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 760 removed outlier: 4.116A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.565A pdb=" N ASN C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.510A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.544A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.515A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.513A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.013A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (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 removed outlier: 3.536A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.800A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.926A pdb=" N GLY H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 131 through 136 removed outlier: 3.572A pdb=" N SER H 134 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.633A pdb=" N VAL H 167 " --> pdb=" O THR H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 removed outlier: 3.823A pdb=" N SER H 207 " --> pdb=" O HIS H 204 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN H 208 " --> pdb=" O LYS H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 208' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.687A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.802A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 189 through 196 removed outlier: 3.597A pdb=" N GLY J 194 " --> pdb=" O SER J 190 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.644A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 128 removed outlier: 4.136A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 154 Processing helix chain 'L' and resid 184 through 190 removed outlier: 4.065A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 190' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.856A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.133A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.172A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.608A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.835A pdb=" N LYS A 310 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY A 601 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.771A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.721A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.845A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 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 Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.436A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.986A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.669A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.771A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.066A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.494A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.928A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.179A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.571A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.967A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.751A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 574 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.258A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 455 removed outlier: 6.835A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 719 " --> pdb=" O VAL B1068 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.734A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.667A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.132A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.562A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.584A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.600A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.236A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.944A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.594A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 541 removed outlier: 3.580A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 13.966A pdb=" N THR C 572 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.764A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.584A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.358A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.648A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS C1083 " --> pdb=" O LYS C1086 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.683A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF3, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.107A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER H 35 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.107A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AF6, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.643A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL H 146 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 139 through 141 removed outlier: 3.971A pdb=" N ALA H 140 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 188 " --> pdb=" O ALA H 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'H' and resid 156 through 158 removed outlier: 4.244A pdb=" N SER H 157 " --> pdb=" O ASN H 201 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN H 201 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.653A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 11 through 14 Processing sheet with id=AG2, first strand: chain 'I' and resid 44 through 46 removed outlier: 3.676A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN I 38 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AG4, first strand: chain 'I' and resid 115 through 119 removed outlier: 3.998A pdb=" N VAL I 134 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL I 134 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU I 180 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU I 136 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER I 178 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN I 138 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU I 176 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N THR I 173 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN I 167 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER I 175 " --> pdb=" O THR I 165 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.829A pdb=" N ALA I 194 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG7, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'J' and resid 44 through 47 removed outlier: 3.646A pdb=" N GLY J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA J 40 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 50 through 51 Processing sheet with id=AH1, first strand: chain 'J' and resid 91 through 93 removed outlier: 3.820A pdb=" N ALA J 91 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL J 113 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.648A pdb=" N LEU J 145 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS J 144 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER J 184 " --> pdb=" O CYS J 144 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP J 148 " --> pdb=" O TYR J 180 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.648A pdb=" N LEU J 145 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS J 144 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER J 184 " --> pdb=" O CYS J 144 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP J 148 " --> pdb=" O TYR J 180 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR J 180 " --> pdb=" O ASP J 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL J 173 " --> pdb=" O SER J 181 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 155 through 157 removed outlier: 3.801A pdb=" N ASN J 203 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER J 157 " --> pdb=" O ASN J 201 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 137 through 140 removed outlier: 5.657A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE L 140 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 146 through 149 1082 hydrogen bonds defined for protein. 2883 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: 8.25 Time building geometry restraints manager: 3.62 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: 5914 1.33 - 1.45: 8803 1.45 - 1.57: 18419 1.57 - 1.69: 1 1.69 - 1.81: 175 Bond restraints: 33312 Sorted by residual: bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.11e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.71e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CB PRO H 151 " pdb=" CG PRO H 151 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.99e+00 bond pdb=" C PRO I 95 " pdb=" N PRO I 96 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.91e+00 ... (remaining 33307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 44703 2.37 - 4.74: 588 4.74 - 7.11: 48 7.11 - 9.48: 7 9.48 - 11.85: 1 Bond angle restraints: 45347 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.91 106.64 5.27 8.90e-01 1.26e+00 3.50e+01 angle pdb=" N VAL B1033 " pdb=" CA VAL B1033 " pdb=" C VAL B1033 " ideal model delta sigma weight residual 113.71 108.93 4.78 9.50e-01 1.11e+00 2.53e+01 angle pdb=" C PRO H 151 " pdb=" N GLU H 152 " pdb=" CA GLU H 152 " ideal model delta sigma weight residual 121.62 129.17 -7.55 1.57e+00 4.06e-01 2.31e+01 angle pdb=" N GLN A 954 " pdb=" CA GLN A 954 " pdb=" CB GLN A 954 " ideal model delta sigma weight residual 110.28 117.41 -7.13 1.55e+00 4.16e-01 2.12e+01 angle pdb=" N PRO H 151 " pdb=" CA PRO H 151 " pdb=" C PRO H 151 " ideal model delta sigma weight residual 112.47 121.16 -8.69 2.06e+00 2.36e-01 1.78e+01 ... (remaining 45342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 19045 20.83 - 41.66: 1091 41.66 - 62.49: 183 62.49 - 83.32: 39 83.32 - 104.15: 14 Dihedral angle restraints: 20372 sinusoidal: 8429 harmonic: 11943 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -136.81 50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA TYR C 904 " pdb=" C TYR C 904 " pdb=" N ARG C 905 " pdb=" CA ARG C 905 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ALA C1070 " pdb=" C ALA C1070 " pdb=" N GLN C1071 " pdb=" CA GLN C1071 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 20369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4486 0.066 - 0.132: 754 0.132 - 0.199: 23 0.199 - 0.265: 9 0.265 - 0.331: 4 Chirality restraints: 5276 Sorted by residual: chirality pdb=" CA PRO H 151 " pdb=" N PRO H 151 " pdb=" C PRO H 151 " pdb=" CB PRO H 151 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE B 569 " pdb=" CA ILE B 569 " pdb=" CG1 ILE B 569 " pdb=" CG2 ILE B 569 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 5273 not shown) Planarity restraints: 5832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 150 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO H 151 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 150 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO J 151 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO J 151 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO J 151 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.054 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO B 987 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.045 5.00e-02 4.00e+02 ... (remaining 5829 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 674 2.66 - 3.22: 31251 3.22 - 3.78: 48957 3.78 - 4.34: 64414 4.34 - 4.90: 102707 Nonbonded interactions: 248003 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.097 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.099 3.040 nonbonded pdb=" OE1 GLN L 125 " pdb=" OG SER L 132 " model vdw 2.101 3.040 nonbonded pdb=" OG SER L 52 " pdb=" O GLY L 64 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR A 741 " pdb=" O LEU A 962 " model vdw 2.143 3.040 ... (remaining 247998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 1307)) selection = (chain 'B' and (resid 14 through 542 or resid 544 through 623 or resid 633 throu \ gh 1307)) selection = (chain 'C' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 542 or resid 544 through 623 or resid 633 through 13 \ 07)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.170 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 33361 Z= 0.158 Angle : 0.671 34.992 45492 Z= 0.347 Chirality : 0.047 0.331 5276 Planarity : 0.005 0.119 5797 Dihedral : 13.683 104.149 12694 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 0.14 % Allowed : 0.17 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4063 helix: 0.86 (0.20), residues: 697 sheet: -0.65 (0.17), residues: 975 loop : -1.23 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.021 0.001 TYR C 904 PHE 0.022 0.001 PHE B 275 TRP 0.043 0.002 TRP I 35 HIS 0.009 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00329 (33312) covalent geometry : angle 0.63936 (45347) SS BOND : bond 0.01406 ( 2) SS BOND : angle 19.18633 ( 4) hydrogen bonds : bond 0.24593 ( 1064) hydrogen bonds : angle 9.40133 ( 2883) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 2.01122 ( 36) link_NAG-ASN : bond 0.00338 ( 35) link_NAG-ASN : angle 1.74962 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 446 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8599 (m110) cc_final: 0.7714 (t0) REVERT: A 197 ILE cc_start: 0.8190 (pt) cc_final: 0.7795 (tt) REVERT: A 198 ASP cc_start: 0.8224 (m-30) cc_final: 0.7601 (p0) REVERT: A 293 LEU cc_start: 0.7674 (tt) cc_final: 0.7406 (tt) REVERT: A 386 LYS cc_start: 0.9145 (tptt) cc_final: 0.8749 (pttt) REVERT: A 387 LEU cc_start: 0.7826 (mt) cc_final: 0.7257 (mt) REVERT: A 563 GLN cc_start: 0.7635 (mt0) cc_final: 0.7348 (mt0) REVERT: A 584 ILE cc_start: 0.9252 (mp) cc_final: 0.9045 (mm) REVERT: A 586 ASP cc_start: 0.7993 (m-30) cc_final: 0.7704 (m-30) REVERT: A 755 GLN cc_start: 0.8850 (mt0) cc_final: 0.8561 (mm-40) REVERT: A 900 MET cc_start: 0.7822 (mmt) cc_final: 0.7303 (mmm) REVERT: A 973 ILE cc_start: 0.9063 (pt) cc_final: 0.8839 (tt) REVERT: A 981 LEU cc_start: 0.8883 (pp) cc_final: 0.8287 (tp) REVERT: A 1082 CYS cc_start: 0.6125 (t) cc_final: 0.5878 (t) REVERT: B 121 ASN cc_start: 0.8451 (m110) cc_final: 0.8218 (p0) REVERT: B 135 PHE cc_start: 0.7822 (m-80) cc_final: 0.7564 (m-80) REVERT: B 297 SER cc_start: 0.9318 (m) cc_final: 0.8917 (p) REVERT: B 386 LYS cc_start: 0.8061 (mttt) cc_final: 0.7096 (tttt) REVERT: B 695 TYR cc_start: 0.9274 (p90) cc_final: 0.8792 (p90) REVERT: B 775 ASP cc_start: 0.8090 (m-30) cc_final: 0.7872 (m-30) REVERT: B 894 LEU cc_start: 0.9567 (mt) cc_final: 0.9250 (mt) REVERT: B 900 MET cc_start: 0.8120 (ttm) cc_final: 0.7896 (tpt) REVERT: C 140 PHE cc_start: 0.6884 (p90) cc_final: 0.6451 (p90) REVERT: C 211 ASN cc_start: 0.8839 (p0) cc_final: 0.8502 (m-40) REVERT: C 221 SER cc_start: 0.8755 (m) cc_final: 0.8532 (p) REVERT: C 242 LEU cc_start: 0.9010 (mm) cc_final: 0.8792 (mm) REVERT: C 582 LEU cc_start: 0.8989 (mp) cc_final: 0.8631 (tt) REVERT: C 614 ASP cc_start: 0.8146 (t0) cc_final: 0.7863 (t70) REVERT: C 699 LEU cc_start: 0.8959 (mm) cc_final: 0.8689 (mm) REVERT: C 968 SER cc_start: 0.9195 (m) cc_final: 0.8829 (p) REVERT: C 970 PHE cc_start: 0.9002 (m-10) cc_final: 0.8527 (m-80) REVERT: H 34 MET cc_start: -0.0094 (ttt) cc_final: -0.1913 (ptp) REVERT: H 104 MET cc_start: 0.0605 (ppp) cc_final: 0.0240 (pmm) REVERT: L 155 LEU cc_start: 0.5202 (tp) cc_final: 0.4845 (tt) outliers start: 5 outliers final: 2 residues processed: 449 average time/residue: 0.1860 time to fit residues: 137.1630 Evaluate side-chains 243 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 580 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN A1005 GLN A1048 HIS B 99 ASN B 149 ASN B 321 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 965 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 613 GLN C 764 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN C 954 GLN C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1119 ASN H 32 ASN H 76 ASN I 90 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 HIS L 156 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.120360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081080 restraints weight = 107018.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075699 restraints weight = 83460.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077292 restraints weight = 89684.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076610 restraints weight = 64023.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076743 restraints weight = 58811.142| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 33361 Z= 0.345 Angle : 0.794 12.219 45492 Z= 0.412 Chirality : 0.051 0.337 5276 Planarity : 0.006 0.118 5797 Dihedral : 8.289 78.869 5399 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 0.28 % Allowed : 5.69 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.13), residues: 4063 helix: 0.29 (0.19), residues: 730 sheet: -0.77 (0.16), residues: 1001 loop : -1.43 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 38 TYR 0.029 0.002 TYR C 904 PHE 0.032 0.003 PHE C 906 TRP 0.021 0.002 TRP A 886 HIS 0.009 0.002 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00765 (33312) covalent geometry : angle 0.78549 (45347) SS BOND : bond 0.00488 ( 2) SS BOND : angle 3.22735 ( 4) hydrogen bonds : bond 0.05717 ( 1064) hydrogen bonds : angle 7.61855 ( 2883) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 2.13446 ( 36) link_NAG-ASN : bond 0.00816 ( 35) link_NAG-ASN : angle 2.21653 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 284 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8328 (mmp80) cc_final: 0.8117 (mmp80) REVERT: A 100 ILE cc_start: 0.9101 (mm) cc_final: 0.8768 (pt) REVERT: A 140 PHE cc_start: 0.8282 (p90) cc_final: 0.7974 (p90) REVERT: A 197 ILE cc_start: 0.8173 (pt) cc_final: 0.7733 (tt) REVERT: A 198 ASP cc_start: 0.8535 (m-30) cc_final: 0.7847 (p0) REVERT: A 386 LYS cc_start: 0.8971 (tptt) cc_final: 0.8608 (pttt) REVERT: A 387 LEU cc_start: 0.8040 (mt) cc_final: 0.7641 (mt) REVERT: A 586 ASP cc_start: 0.8148 (m-30) cc_final: 0.7843 (m-30) REVERT: A 755 GLN cc_start: 0.9261 (mt0) cc_final: 0.8581 (mm-40) REVERT: A 981 LEU cc_start: 0.9132 (pp) cc_final: 0.8810 (tp) REVERT: A 988 GLU cc_start: 0.8445 (tp30) cc_final: 0.8123 (tp30) REVERT: B 81 ASN cc_start: 0.8683 (t0) cc_final: 0.8474 (t0) REVERT: B 133 PHE cc_start: 0.8318 (m-10) cc_final: 0.8049 (m-80) REVERT: B 135 PHE cc_start: 0.7688 (m-80) cc_final: 0.7368 (m-10) REVERT: B 223 LEU cc_start: 0.9207 (mp) cc_final: 0.8964 (mp) REVERT: B 293 LEU cc_start: 0.9329 (tt) cc_final: 0.8984 (mm) REVERT: B 386 LYS cc_start: 0.8774 (mttt) cc_final: 0.7579 (tttt) REVERT: B 695 TYR cc_start: 0.9553 (p90) cc_final: 0.9007 (p90) REVERT: B 740 MET cc_start: 0.9253 (ttm) cc_final: 0.9018 (mtp) REVERT: B 900 MET cc_start: 0.8877 (ttm) cc_final: 0.8247 (tpt) REVERT: B 928 ASN cc_start: 0.8971 (m-40) cc_final: 0.8746 (m-40) REVERT: C 104 TRP cc_start: 0.8850 (m-90) cc_final: 0.8460 (m-10) REVERT: C 121 ASN cc_start: 0.7903 (m-40) cc_final: 0.6519 (p0) REVERT: C 140 PHE cc_start: 0.7110 (p90) cc_final: 0.6394 (p90) REVERT: C 196 ASN cc_start: 0.7920 (t0) cc_final: 0.7343 (p0) REVERT: C 211 ASN cc_start: 0.9054 (p0) cc_final: 0.8654 (m-40) REVERT: C 212 LEU cc_start: 0.8264 (tp) cc_final: 0.7945 (tt) REVERT: C 439 ASN cc_start: 0.8779 (t0) cc_final: 0.8530 (m-40) REVERT: C 614 ASP cc_start: 0.8124 (t0) cc_final: 0.7769 (t70) REVERT: C 699 LEU cc_start: 0.9059 (mm) cc_final: 0.8841 (mm) REVERT: C 968 SER cc_start: 0.9109 (m) cc_final: 0.8908 (t) REVERT: H 34 MET cc_start: 0.0786 (ttt) cc_final: -0.1593 (ptp) REVERT: H 104 MET cc_start: 0.2612 (ppp) cc_final: 0.1259 (mtm) REVERT: J 82 MET cc_start: -0.0637 (mtm) cc_final: -0.1515 (mtm) REVERT: J 104 MET cc_start: 0.1818 (mmp) cc_final: -0.0130 (tpp) outliers start: 10 outliers final: 1 residues processed: 294 average time/residue: 0.1830 time to fit residues: 91.4271 Evaluate side-chains 195 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 76 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 406 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 389 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 chunk 310 optimal weight: 0.9980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 926 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 334 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN C1036 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** I 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 148 GLN J 81 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.118880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080540 restraints weight = 107632.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076215 restraints weight = 85933.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077675 restraints weight = 89294.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077086 restraints weight = 63203.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077815 restraints weight = 56035.121| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 33361 Z= 0.319 Angle : 0.764 13.307 45492 Z= 0.395 Chirality : 0.051 0.327 5276 Planarity : 0.006 0.119 5797 Dihedral : 7.792 77.887 5399 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.87 % Favored : 93.03 % Rotamer: Outliers : 0.20 % Allowed : 5.97 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.13), residues: 4063 helix: 0.07 (0.19), residues: 720 sheet: -0.88 (0.16), residues: 997 loop : -1.56 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.028 0.002 TYR C 904 PHE 0.032 0.003 PHE A1052 TRP 0.019 0.002 TRP J 47 HIS 0.011 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00705 (33312) covalent geometry : angle 0.75440 (45347) SS BOND : bond 0.02563 ( 2) SS BOND : angle 2.57194 ( 4) hydrogen bonds : bond 0.05248 ( 1064) hydrogen bonds : angle 7.11951 ( 2883) link_BETA1-4 : bond 0.00394 ( 12) link_BETA1-4 : angle 2.43519 ( 36) link_NAG-ASN : bond 0.00748 ( 35) link_NAG-ASN : angle 2.26098 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 247 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8342 (mmp80) cc_final: 0.7457 (mpp-170) REVERT: A 100 ILE cc_start: 0.9026 (mm) cc_final: 0.8772 (pt) REVERT: A 140 PHE cc_start: 0.8367 (p90) cc_final: 0.7975 (p90) REVERT: A 144 TYR cc_start: 0.3881 (p90) cc_final: 0.3249 (p90) REVERT: A 197 ILE cc_start: 0.8190 (pt) cc_final: 0.7901 (tt) REVERT: A 386 LYS cc_start: 0.8911 (tptt) cc_final: 0.8609 (pttt) REVERT: A 586 ASP cc_start: 0.8051 (m-30) cc_final: 0.7762 (m-30) REVERT: B 81 ASN cc_start: 0.8735 (t0) cc_final: 0.8485 (t0) REVERT: B 135 PHE cc_start: 0.7565 (m-80) cc_final: 0.7298 (m-10) REVERT: B 238 PHE cc_start: 0.7984 (p90) cc_final: 0.7777 (p90) REVERT: B 386 LYS cc_start: 0.8856 (mttt) cc_final: 0.7656 (tttt) REVERT: B 387 LEU cc_start: 0.8974 (mp) cc_final: 0.8770 (mp) REVERT: B 695 TYR cc_start: 0.9565 (p90) cc_final: 0.9147 (p90) REVERT: B 740 MET cc_start: 0.9054 (ttm) cc_final: 0.8836 (mtp) REVERT: B 794 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6646 (tp) REVERT: C 211 ASN cc_start: 0.8974 (p0) cc_final: 0.8634 (m-40) REVERT: C 439 ASN cc_start: 0.8747 (t0) cc_final: 0.8516 (m-40) REVERT: C 614 ASP cc_start: 0.8128 (t0) cc_final: 0.7782 (t70) REVERT: C 671 CYS cc_start: 0.6859 (m) cc_final: 0.5713 (m) REVERT: C 803 SER cc_start: 0.8972 (p) cc_final: 0.8474 (t) REVERT: C 969 ASN cc_start: 0.9468 (p0) cc_final: 0.9155 (p0) REVERT: H 34 MET cc_start: 0.0362 (ttt) cc_final: -0.1163 (ptp) REVERT: I 148 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.6059 (pm20) REVERT: J 82 MET cc_start: -0.0065 (mtm) cc_final: -0.0861 (mtm) outliers start: 7 outliers final: 3 residues processed: 254 average time/residue: 0.1696 time to fit residues: 73.7224 Evaluate side-chains 179 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 341 optimal weight: 50.0000 chunk 343 optimal weight: 9.9990 chunk 404 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 99 ASN B 121 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS I 55 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.119527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080423 restraints weight = 106024.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076052 restraints weight = 81262.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077490 restraints weight = 85684.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077154 restraints weight = 60070.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078256 restraints weight = 52978.767| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 33361 Z= 0.266 Angle : 0.715 12.266 45492 Z= 0.367 Chirality : 0.050 0.322 5276 Planarity : 0.005 0.121 5797 Dihedral : 7.544 78.459 5399 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.40 % Favored : 93.50 % Rotamer: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.13), residues: 4063 helix: 0.13 (0.19), residues: 728 sheet: -0.91 (0.16), residues: 981 loop : -1.53 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 34 TYR 0.041 0.002 TYR L 87 PHE 0.025 0.002 PHE B 275 TRP 0.017 0.002 TRP C 633 HIS 0.010 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00597 (33312) covalent geometry : angle 0.70341 (45347) SS BOND : bond 0.01187 ( 2) SS BOND : angle 2.61912 ( 4) hydrogen bonds : bond 0.04806 ( 1064) hydrogen bonds : angle 6.79721 ( 2883) link_BETA1-4 : bond 0.00400 ( 12) link_BETA1-4 : angle 2.43283 ( 36) link_NAG-ASN : bond 0.00662 ( 35) link_NAG-ASN : angle 2.34533 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8399 (mmp80) cc_final: 0.7486 (mpp-170) REVERT: A 55 PHE cc_start: 0.8112 (m-10) cc_final: 0.7767 (m-10) REVERT: A 100 ILE cc_start: 0.9103 (mm) cc_final: 0.8864 (pt) REVERT: A 104 TRP cc_start: 0.8704 (m-90) cc_final: 0.8357 (m-90) REVERT: A 135 PHE cc_start: 0.8465 (m-80) cc_final: 0.8035 (m-80) REVERT: A 140 PHE cc_start: 0.8328 (p90) cc_final: 0.7926 (p90) REVERT: A 197 ILE cc_start: 0.8277 (pt) cc_final: 0.8036 (tt) REVERT: A 386 LYS cc_start: 0.8903 (tptt) cc_final: 0.8619 (pttt) REVERT: A 586 ASP cc_start: 0.8031 (m-30) cc_final: 0.7703 (m-30) REVERT: A 904 TYR cc_start: 0.7547 (t80) cc_final: 0.6641 (t80) REVERT: B 81 ASN cc_start: 0.8915 (t0) cc_final: 0.8630 (t0) REVERT: B 135 PHE cc_start: 0.7473 (m-80) cc_final: 0.7174 (m-10) REVERT: B 386 LYS cc_start: 0.8874 (mttt) cc_final: 0.7545 (tttt) REVERT: B 695 TYR cc_start: 0.9564 (p90) cc_final: 0.9247 (p90) REVERT: B 900 MET cc_start: 0.8910 (ttm) cc_final: 0.8418 (tpp) REVERT: C 121 ASN cc_start: 0.7418 (m-40) cc_final: 0.6712 (p0) REVERT: C 177 MET cc_start: 0.6279 (mmt) cc_final: 0.5862 (mmm) REVERT: C 211 ASN cc_start: 0.8940 (p0) cc_final: 0.8591 (m-40) REVERT: C 212 LEU cc_start: 0.8321 (tp) cc_final: 0.8001 (tt) REVERT: C 238 PHE cc_start: 0.8642 (p90) cc_final: 0.8424 (p90) REVERT: C 900 MET cc_start: 0.8834 (mtm) cc_final: 0.8495 (mtt) REVERT: C 969 ASN cc_start: 0.9448 (p0) cc_final: 0.9107 (p0) REVERT: H 34 MET cc_start: -0.0337 (ttt) cc_final: -0.1201 (ptp) REVERT: J 82 MET cc_start: 0.0091 (mtm) cc_final: -0.0552 (mtm) REVERT: J 180 TYR cc_start: 0.8396 (m-10) cc_final: 0.8021 (m-10) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1804 time to fit residues: 74.8846 Evaluate side-chains 165 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 320 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 392 optimal weight: 0.0040 chunk 240 optimal weight: 3.9990 chunk 375 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 379 optimal weight: 50.0000 chunk 197 optimal weight: 10.0000 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN C1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.121353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081684 restraints weight = 105021.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.077889 restraints weight = 77405.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078613 restraints weight = 76425.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078750 restraints weight = 52984.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079522 restraints weight = 50719.251| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 33361 Z= 0.169 Angle : 0.631 10.063 45492 Z= 0.321 Chirality : 0.048 0.333 5276 Planarity : 0.005 0.123 5797 Dihedral : 7.136 78.668 5399 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4063 helix: 0.59 (0.20), residues: 719 sheet: -0.85 (0.16), residues: 986 loop : -1.42 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.027 0.001 TYR C 904 PHE 0.021 0.002 PHE C 888 TRP 0.021 0.002 TRP B 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00384 (33312) covalent geometry : angle 0.61934 (45347) SS BOND : bond 0.00683 ( 2) SS BOND : angle 3.02220 ( 4) hydrogen bonds : bond 0.04359 ( 1064) hydrogen bonds : angle 6.41889 ( 2883) link_BETA1-4 : bond 0.00226 ( 12) link_BETA1-4 : angle 2.28536 ( 36) link_NAG-ASN : bond 0.00408 ( 35) link_NAG-ASN : angle 2.16267 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8406 (mmp80) cc_final: 0.7512 (mpp-170) REVERT: A 100 ILE cc_start: 0.9086 (mm) cc_final: 0.8804 (pt) REVERT: A 135 PHE cc_start: 0.8240 (m-80) cc_final: 0.7836 (m-80) REVERT: A 140 PHE cc_start: 0.8330 (p90) cc_final: 0.7891 (p90) REVERT: A 197 ILE cc_start: 0.8228 (pt) cc_final: 0.8022 (tt) REVERT: A 386 LYS cc_start: 0.8919 (tptt) cc_final: 0.8655 (pttt) REVERT: A 584 ILE cc_start: 0.9349 (mm) cc_final: 0.9142 (mm) REVERT: A 586 ASP cc_start: 0.8060 (m-30) cc_final: 0.7726 (m-30) REVERT: A 904 TYR cc_start: 0.7320 (t80) cc_final: 0.6465 (t80) REVERT: A 965 GLN cc_start: 0.9163 (tp40) cc_final: 0.8312 (tp-100) REVERT: A 968 SER cc_start: 0.8938 (t) cc_final: 0.8462 (t) REVERT: A 981 LEU cc_start: 0.8992 (pp) cc_final: 0.8655 (tp) REVERT: A 1048 HIS cc_start: 0.8757 (t-170) cc_final: 0.8546 (t-170) REVERT: B 81 ASN cc_start: 0.8919 (t0) cc_final: 0.8655 (t0) REVERT: B 135 PHE cc_start: 0.7490 (m-80) cc_final: 0.7152 (m-10) REVERT: B 386 LYS cc_start: 0.8860 (mttt) cc_final: 0.7657 (tttt) REVERT: B 518 LEU cc_start: 0.6086 (tt) cc_final: 0.5762 (mm) REVERT: B 695 TYR cc_start: 0.9496 (p90) cc_final: 0.9168 (p90) REVERT: B 900 MET cc_start: 0.8841 (ttm) cc_final: 0.8291 (tpp) REVERT: B 928 ASN cc_start: 0.8911 (m-40) cc_final: 0.8628 (m110) REVERT: C 121 ASN cc_start: 0.7381 (m-40) cc_final: 0.6883 (p0) REVERT: C 177 MET cc_start: 0.6347 (mmt) cc_final: 0.5922 (mmm) REVERT: C 211 ASN cc_start: 0.8945 (p0) cc_final: 0.8650 (m-40) REVERT: C 212 LEU cc_start: 0.8353 (tp) cc_final: 0.8005 (tt) REVERT: C 444 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6915 (mmtm) REVERT: C 519 HIS cc_start: 0.7935 (p90) cc_final: 0.7701 (p90) REVERT: C 900 MET cc_start: 0.8886 (mtm) cc_final: 0.8586 (mtt) REVERT: C 969 ASN cc_start: 0.9440 (p0) cc_final: 0.9137 (p0) REVERT: H 34 MET cc_start: -0.0769 (ttt) cc_final: -0.1512 (ptp) REVERT: L 110 THR cc_start: 0.5939 (p) cc_final: 0.4959 (p) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1735 time to fit residues: 75.3662 Evaluate side-chains 177 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 383 optimal weight: 50.0000 chunk 66 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1101 HIS B 99 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1036 GLN H 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.122559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075032 restraints weight = 104481.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074843 restraints weight = 75921.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076175 restraints weight = 53045.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.075978 restraints weight = 47540.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076197 restraints weight = 40921.234| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 33361 Z= 0.137 Angle : 0.606 9.970 45492 Z= 0.307 Chirality : 0.047 0.319 5276 Planarity : 0.005 0.126 5797 Dihedral : 6.859 78.761 5399 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 0.03 % Allowed : 1.79 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4063 helix: 0.75 (0.20), residues: 721 sheet: -0.81 (0.16), residues: 1010 loop : -1.29 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.022 0.001 TYR C 904 PHE 0.028 0.001 PHE B 275 TRP 0.019 0.001 TRP B 886 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00314 (33312) covalent geometry : angle 0.59451 (45347) SS BOND : bond 0.00471 ( 2) SS BOND : angle 2.79984 ( 4) hydrogen bonds : bond 0.04116 ( 1064) hydrogen bonds : angle 6.16626 ( 2883) link_BETA1-4 : bond 0.00297 ( 12) link_BETA1-4 : angle 2.15179 ( 36) link_NAG-ASN : bond 0.00516 ( 35) link_NAG-ASN : angle 2.10234 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8327 (mmp80) cc_final: 0.7442 (mpp-170) REVERT: A 100 ILE cc_start: 0.9205 (mm) cc_final: 0.8904 (pt) REVERT: A 135 PHE cc_start: 0.8289 (m-80) cc_final: 0.7896 (m-80) REVERT: A 140 PHE cc_start: 0.8226 (p90) cc_final: 0.7621 (p90) REVERT: A 177 MET cc_start: 0.5803 (pmm) cc_final: 0.4986 (pmm) REVERT: A 197 ILE cc_start: 0.8328 (pt) cc_final: 0.8107 (tt) REVERT: A 386 LYS cc_start: 0.8947 (tptt) cc_final: 0.8699 (pttt) REVERT: A 584 ILE cc_start: 0.9218 (mm) cc_final: 0.8955 (mm) REVERT: A 904 TYR cc_start: 0.7275 (t80) cc_final: 0.6558 (t80) REVERT: A 965 GLN cc_start: 0.9138 (tp40) cc_final: 0.8682 (tp-100) REVERT: A 968 SER cc_start: 0.8846 (t) cc_final: 0.8645 (t) REVERT: A 981 LEU cc_start: 0.9006 (pp) cc_final: 0.8777 (tp) REVERT: B 81 ASN cc_start: 0.9031 (t0) cc_final: 0.8753 (t0) REVERT: B 242 LEU cc_start: 0.8757 (mt) cc_final: 0.8552 (mt) REVERT: B 297 SER cc_start: 0.9355 (m) cc_final: 0.8978 (p) REVERT: B 386 LYS cc_start: 0.8697 (mttt) cc_final: 0.7453 (tttt) REVERT: B 695 TYR cc_start: 0.9511 (p90) cc_final: 0.9108 (p90) REVERT: B 928 ASN cc_start: 0.8857 (m-40) cc_final: 0.8543 (m-40) REVERT: C 121 ASN cc_start: 0.7481 (m-40) cc_final: 0.7141 (p0) REVERT: C 177 MET cc_start: 0.6048 (mmt) cc_final: 0.5687 (mmm) REVERT: C 211 ASN cc_start: 0.9076 (p0) cc_final: 0.8802 (m-40) REVERT: C 212 LEU cc_start: 0.8428 (tp) cc_final: 0.8052 (tt) REVERT: C 238 PHE cc_start: 0.8795 (p90) cc_final: 0.8557 (p90) REVERT: C 900 MET cc_start: 0.9009 (mtm) cc_final: 0.8697 (mtm) REVERT: C 969 ASN cc_start: 0.9405 (p0) cc_final: 0.9121 (p0) REVERT: H 34 MET cc_start: -0.0884 (ttt) cc_final: -0.1923 (ptp) REVERT: J 109 ARG cc_start: 0.6538 (mmp-170) cc_final: 0.6052 (mmp-170) REVERT: L 110 THR cc_start: 0.7181 (p) cc_final: 0.6620 (p) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1822 time to fit residues: 77.6740 Evaluate side-chains 180 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 127 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 385 optimal weight: 0.0870 chunk 151 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 176 optimal weight: 0.3980 overall best weight: 2.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN I 190 HIS J 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.120089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081220 restraints weight = 107091.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077156 restraints weight = 82052.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.077718 restraints weight = 82120.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.078420 restraints weight = 55732.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078556 restraints weight = 49863.418| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 33361 Z= 0.239 Angle : 0.673 10.197 45492 Z= 0.345 Chirality : 0.048 0.313 5276 Planarity : 0.005 0.126 5797 Dihedral : 7.082 78.919 5399 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 4063 helix: 0.47 (0.19), residues: 724 sheet: -0.90 (0.16), residues: 995 loop : -1.38 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 319 TYR 0.025 0.002 TYR H 94 PHE 0.025 0.002 PHE B 275 TRP 0.018 0.002 TRP B 886 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00537 (33312) covalent geometry : angle 0.66276 (45347) SS BOND : bond 0.00777 ( 2) SS BOND : angle 2.48100 ( 4) hydrogen bonds : bond 0.04430 ( 1064) hydrogen bonds : angle 6.35634 ( 2883) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 2.32679 ( 36) link_NAG-ASN : bond 0.00577 ( 35) link_NAG-ASN : angle 2.14012 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8354 (mmp80) cc_final: 0.7449 (mpp-170) REVERT: A 100 ILE cc_start: 0.9128 (mm) cc_final: 0.8848 (pt) REVERT: A 135 PHE cc_start: 0.8214 (m-80) cc_final: 0.7923 (m-80) REVERT: A 140 PHE cc_start: 0.8364 (p90) cc_final: 0.7944 (p90) REVERT: A 197 ILE cc_start: 0.8285 (pt) cc_final: 0.8054 (tt) REVERT: A 386 LYS cc_start: 0.8918 (tptt) cc_final: 0.8628 (pttt) REVERT: A 900 MET cc_start: 0.8226 (mmt) cc_final: 0.7904 (mmm) REVERT: A 904 TYR cc_start: 0.7601 (t80) cc_final: 0.6805 (t80) REVERT: A 981 LEU cc_start: 0.8985 (pp) cc_final: 0.8698 (tp) REVERT: B 133 PHE cc_start: 0.8077 (m-80) cc_final: 0.6639 (m-80) REVERT: B 386 LYS cc_start: 0.8822 (mttt) cc_final: 0.7482 (tttt) REVERT: B 695 TYR cc_start: 0.9539 (p90) cc_final: 0.9252 (p90) REVERT: B 900 MET cc_start: 0.8802 (ttm) cc_final: 0.8306 (tpp) REVERT: B 928 ASN cc_start: 0.8879 (m-40) cc_final: 0.8644 (m-40) REVERT: C 121 ASN cc_start: 0.7460 (m-40) cc_final: 0.7181 (p0) REVERT: C 177 MET cc_start: 0.6208 (mmt) cc_final: 0.5737 (mmm) REVERT: C 211 ASN cc_start: 0.8885 (p0) cc_final: 0.8647 (m-40) REVERT: C 212 LEU cc_start: 0.8415 (tp) cc_final: 0.8044 (tt) REVERT: C 238 PHE cc_start: 0.8698 (p90) cc_final: 0.8485 (p90) REVERT: C 697 MET cc_start: 0.8126 (tpt) cc_final: 0.7910 (tpt) REVERT: C 900 MET cc_start: 0.9041 (mtm) cc_final: 0.8780 (mtm) REVERT: C 969 ASN cc_start: 0.9447 (p0) cc_final: 0.9137 (p0) REVERT: H 34 MET cc_start: -0.0899 (ttt) cc_final: -0.1625 (ptm) REVERT: J 109 ARG cc_start: 0.6552 (mmp-170) cc_final: 0.5983 (mmp-170) REVERT: L 110 THR cc_start: 0.6396 (p) cc_final: 0.5139 (p) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1778 time to fit residues: 69.6253 Evaluate side-chains 171 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 179 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 306 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 367 optimal weight: 40.0000 chunk 294 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.147095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097881 restraints weight = 87911.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096226 restraints weight = 72251.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096613 restraints weight = 57390.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096729 restraints weight = 53253.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096901 restraints weight = 48652.434| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 33361 Z= 0.168 Angle : 0.624 10.128 45492 Z= 0.317 Chirality : 0.047 0.311 5276 Planarity : 0.005 0.127 5797 Dihedral : 6.870 79.189 5399 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 1.00 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4063 helix: 0.61 (0.20), residues: 725 sheet: -0.88 (0.16), residues: 1008 loop : -1.34 (0.13), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 143 TYR 0.023 0.001 TYR C 904 PHE 0.022 0.002 PHE B 275 TRP 0.018 0.001 TRP B 886 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00382 (33312) covalent geometry : angle 0.61448 (45347) SS BOND : bond 0.00257 ( 2) SS BOND : angle 2.73438 ( 4) hydrogen bonds : bond 0.04180 ( 1064) hydrogen bonds : angle 6.12552 ( 2883) link_BETA1-4 : bond 0.00280 ( 12) link_BETA1-4 : angle 2.24756 ( 36) link_NAG-ASN : bond 0.00394 ( 35) link_NAG-ASN : angle 1.96963 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8329 (mmp80) cc_final: 0.7476 (mpp-170) REVERT: A 100 ILE cc_start: 0.9123 (mm) cc_final: 0.8815 (pt) REVERT: A 121 ASN cc_start: 0.8774 (m-40) cc_final: 0.7408 (t0) REVERT: A 135 PHE cc_start: 0.8031 (m-80) cc_final: 0.7806 (m-80) REVERT: A 140 PHE cc_start: 0.8220 (p90) cc_final: 0.7726 (p90) REVERT: A 177 MET cc_start: 0.5386 (pmm) cc_final: 0.4247 (pmm) REVERT: A 197 ILE cc_start: 0.8473 (pt) cc_final: 0.8233 (tt) REVERT: A 386 LYS cc_start: 0.8972 (tptt) cc_final: 0.8708 (pttt) REVERT: A 697 MET cc_start: 0.8863 (tpt) cc_final: 0.8500 (tpt) REVERT: A 904 TYR cc_start: 0.7288 (t80) cc_final: 0.6612 (t80) REVERT: B 81 ASN cc_start: 0.8938 (t0) cc_final: 0.8561 (t0) REVERT: B 133 PHE cc_start: 0.8225 (m-80) cc_final: 0.6825 (m-80) REVERT: B 238 PHE cc_start: 0.8505 (p90) cc_final: 0.7739 (p90) REVERT: B 386 LYS cc_start: 0.8765 (mttt) cc_final: 0.7386 (tttt) REVERT: B 695 TYR cc_start: 0.9498 (p90) cc_final: 0.9138 (p90) REVERT: B 928 ASN cc_start: 0.8784 (m-40) cc_final: 0.8516 (m-40) REVERT: C 177 MET cc_start: 0.5817 (mmt) cc_final: 0.5497 (mmm) REVERT: C 211 ASN cc_start: 0.8785 (p0) cc_final: 0.8552 (m-40) REVERT: C 212 LEU cc_start: 0.8342 (tp) cc_final: 0.7954 (tt) REVERT: C 238 PHE cc_start: 0.8618 (p90) cc_final: 0.8375 (p90) REVERT: C 969 ASN cc_start: 0.9402 (p0) cc_final: 0.9097 (p0) REVERT: H 34 MET cc_start: -0.0922 (ttt) cc_final: -0.1686 (ptm) REVERT: J 82 MET cc_start: -0.0897 (mtm) cc_final: -0.1766 (mtm) REVERT: J 109 ARG cc_start: 0.6604 (mmp-170) cc_final: 0.6118 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1759 time to fit residues: 72.6508 Evaluate side-chains 177 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 306 optimal weight: 1.9990 chunk 400 optimal weight: 9.9990 chunk 389 optimal weight: 20.0000 chunk 323 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 284 optimal weight: 3.9990 chunk 301 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.119987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.073787 restraints weight = 106638.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.071881 restraints weight = 89103.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073101 restraints weight = 67083.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073084 restraints weight = 59580.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073550 restraints weight = 49678.022| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 33361 Z= 0.217 Angle : 0.664 10.306 45492 Z= 0.339 Chirality : 0.048 0.313 5276 Planarity : 0.005 0.127 5797 Dihedral : 6.958 79.320 5399 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.13 % Rotamer: Outliers : 0.03 % Allowed : 0.70 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4063 helix: 0.48 (0.19), residues: 728 sheet: -0.85 (0.16), residues: 992 loop : -1.39 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 143 TYR 0.023 0.002 TYR C 904 PHE 0.035 0.002 PHE B 275 TRP 0.017 0.002 TRP A 104 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00490 (33312) covalent geometry : angle 0.65396 (45347) SS BOND : bond 0.00703 ( 2) SS BOND : angle 2.35036 ( 4) hydrogen bonds : bond 0.04362 ( 1064) hydrogen bonds : angle 6.19486 ( 2883) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 2.31292 ( 36) link_NAG-ASN : bond 0.00525 ( 35) link_NAG-ASN : angle 2.06839 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8271 (mmp80) cc_final: 0.7432 (mpp-170) REVERT: A 121 ASN cc_start: 0.8899 (m-40) cc_final: 0.7539 (t0) REVERT: A 135 PHE cc_start: 0.8235 (m-80) cc_final: 0.8005 (m-80) REVERT: A 140 PHE cc_start: 0.8267 (p90) cc_final: 0.7682 (p90) REVERT: A 177 MET cc_start: 0.5775 (pmm) cc_final: 0.4731 (pmm) REVERT: A 197 ILE cc_start: 0.8260 (pt) cc_final: 0.8033 (tt) REVERT: A 697 MET cc_start: 0.8866 (tpt) cc_final: 0.8399 (tpt) REVERT: A 900 MET cc_start: 0.8462 (mmt) cc_final: 0.8143 (mmm) REVERT: A 904 TYR cc_start: 0.7340 (t80) cc_final: 0.6657 (t80) REVERT: B 133 PHE cc_start: 0.8033 (m-80) cc_final: 0.6558 (m-80) REVERT: B 242 LEU cc_start: 0.8728 (mt) cc_final: 0.8485 (mt) REVERT: B 386 LYS cc_start: 0.8717 (mttt) cc_final: 0.7362 (tttt) REVERT: B 695 TYR cc_start: 0.9524 (p90) cc_final: 0.9209 (p90) REVERT: B 928 ASN cc_start: 0.8922 (m-40) cc_final: 0.8646 (m110) REVERT: B 969 ASN cc_start: 0.9073 (p0) cc_final: 0.8666 (p0) REVERT: C 177 MET cc_start: 0.5472 (mmt) cc_final: 0.5209 (mmm) REVERT: C 211 ASN cc_start: 0.9020 (p0) cc_final: 0.8690 (m-40) REVERT: C 212 LEU cc_start: 0.8524 (tp) cc_final: 0.8156 (tt) REVERT: C 238 PHE cc_start: 0.8776 (p90) cc_final: 0.8481 (p90) REVERT: C 900 MET cc_start: 0.8820 (mtm) cc_final: 0.8503 (mtt) REVERT: C 969 ASN cc_start: 0.9440 (p0) cc_final: 0.9110 (p0) REVERT: C 984 LEU cc_start: 0.8940 (mt) cc_final: 0.8584 (tp) REVERT: H 34 MET cc_start: -0.1443 (ttt) cc_final: -0.1804 (ptm) REVERT: J 82 MET cc_start: -0.1196 (mtm) cc_final: -0.1973 (mtm) REVERT: J 109 ARG cc_start: 0.6460 (mmp-170) cc_final: 0.5907 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1792 time to fit residues: 70.1280 Evaluate side-chains 165 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 277 optimal weight: 0.9990 chunk 165 optimal weight: 0.0050 chunk 292 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 212 optimal weight: 0.0970 chunk 364 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** H 39 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 = 0.4019 r_free = 0.4019 target = 0.122039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.073658 restraints weight = 105109.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074009 restraints weight = 79457.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075219 restraints weight = 51362.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075302 restraints weight = 42231.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075497 restraints weight = 38947.251| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 33361 Z= 0.135 Angle : 0.611 10.884 45492 Z= 0.309 Chirality : 0.047 0.310 5276 Planarity : 0.005 0.128 5797 Dihedral : 6.679 79.392 5399 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 0.03 % Allowed : 0.14 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4063 helix: 0.70 (0.20), residues: 730 sheet: -0.78 (0.16), residues: 990 loop : -1.25 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 143 TYR 0.025 0.001 TYR L 87 PHE 0.030 0.002 PHE B 275 TRP 0.016 0.001 TRP C 633 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00311 (33312) covalent geometry : angle 0.59865 (45347) SS BOND : bond 0.00367 ( 2) SS BOND : angle 2.46162 ( 4) hydrogen bonds : bond 0.04061 ( 1064) hydrogen bonds : angle 5.89507 ( 2883) link_BETA1-4 : bond 0.00297 ( 12) link_BETA1-4 : angle 2.16280 ( 36) link_NAG-ASN : bond 0.00322 ( 35) link_NAG-ASN : angle 2.30019 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8126 Ramachandran restraints generated. 4063 Oldfield, 0 Emsley, 4063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8265 (mmp80) cc_final: 0.7427 (mpp-170) REVERT: A 55 PHE cc_start: 0.8020 (m-10) cc_final: 0.7733 (m-10) REVERT: A 135 PHE cc_start: 0.8157 (m-80) cc_final: 0.7926 (m-80) REVERT: A 140 PHE cc_start: 0.8171 (p90) cc_final: 0.7521 (p90) REVERT: A 144 TYR cc_start: 0.3777 (p90) cc_final: 0.3576 (p90) REVERT: A 197 ILE cc_start: 0.8305 (pt) cc_final: 0.8075 (tt) REVERT: A 386 LYS cc_start: 0.9005 (tptt) cc_final: 0.8731 (pttt) REVERT: A 697 MET cc_start: 0.8780 (tpt) cc_final: 0.8464 (tpt) REVERT: A 740 MET cc_start: 0.9342 (ppp) cc_final: 0.9114 (ppp) REVERT: A 819 GLU cc_start: 0.8849 (pt0) cc_final: 0.8566 (pm20) REVERT: A 900 MET cc_start: 0.8272 (mmt) cc_final: 0.8019 (mmm) REVERT: A 904 TYR cc_start: 0.7267 (t80) cc_final: 0.6543 (t80) REVERT: A 1029 MET cc_start: 0.8950 (tpt) cc_final: 0.8495 (tpt) REVERT: B 133 PHE cc_start: 0.7930 (m-80) cc_final: 0.6589 (m-80) REVERT: B 242 LEU cc_start: 0.8668 (mt) cc_final: 0.8462 (mt) REVERT: B 297 SER cc_start: 0.9324 (m) cc_final: 0.8982 (p) REVERT: B 386 LYS cc_start: 0.8625 (mttt) cc_final: 0.7308 (tttt) REVERT: B 695 TYR cc_start: 0.9456 (p90) cc_final: 0.9207 (p90) REVERT: B 900 MET cc_start: 0.8468 (ttm) cc_final: 0.8144 (tpp) REVERT: B 928 ASN cc_start: 0.8865 (m-40) cc_final: 0.8574 (m-40) REVERT: B 969 ASN cc_start: 0.9036 (p0) cc_final: 0.8657 (p0) REVERT: C 211 ASN cc_start: 0.9005 (p0) cc_final: 0.8701 (m-40) REVERT: C 212 LEU cc_start: 0.8552 (tp) cc_final: 0.8179 (tt) REVERT: C 238 PHE cc_start: 0.8747 (p90) cc_final: 0.8470 (p90) REVERT: C 270 LEU cc_start: 0.7277 (mt) cc_final: 0.6951 (mt) REVERT: C 538 CYS cc_start: 0.8548 (p) cc_final: 0.8335 (p) REVERT: C 900 MET cc_start: 0.8773 (mtm) cc_final: 0.8303 (mtt) REVERT: C 969 ASN cc_start: 0.9419 (p0) cc_final: 0.9121 (p0) REVERT: C 984 LEU cc_start: 0.8991 (mt) cc_final: 0.8668 (tp) REVERT: J 82 MET cc_start: -0.1385 (mtm) cc_final: -0.2096 (mtm) REVERT: J 109 ARG cc_start: 0.6652 (mmp-170) cc_final: 0.6055 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1780 time to fit residues: 72.8394 Evaluate side-chains 183 residues out of total 3585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 335 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 388 optimal weight: 8.9990 chunk 383 optimal weight: 6.9990 chunk 393 optimal weight: 50.0000 chunk 376 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 373 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 371 optimal weight: 10.0000 chunk 304 optimal weight: 0.3980 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 487 ASN C 751 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN H 196 GLN L 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.116954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078349 restraints weight = 106557.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.073065 restraints weight = 89372.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.073723 restraints weight = 90878.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074417 restraints weight = 61024.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.074422 restraints weight = 54543.078| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.143 33361 Z= 0.391 Angle : 0.853 13.140 45492 Z= 0.438 Chirality : 0.053 0.317 5276 Planarity : 0.006 0.127 5797 Dihedral : 7.630 79.634 5399 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.34 % Favored : 91.58 % Rotamer: Outliers : 0.03 % Allowed : 0.64 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.13), residues: 4063 helix: -0.26 (0.18), residues: 737 sheet: -0.91 (0.16), residues: 967 loop : -1.62 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 190 TYR 0.030 0.002 TYR B 873 PHE 0.042 0.003 PHE C 802 TRP 0.026 0.002 TRP A 104 HIS 0.013 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00872 (33312) covalent geometry : angle 0.84091 (45347) SS BOND : bond 0.01300 ( 2) SS BOND : angle 2.41046 ( 4) hydrogen bonds : bond 0.05213 ( 1064) hydrogen bonds : angle 6.71446 ( 2883) link_BETA1-4 : bond 0.00579 ( 12) link_BETA1-4 : angle 2.76909 ( 36) link_NAG-ASN : bond 0.00985 ( 35) link_NAG-ASN : angle 2.67333 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4799.93 seconds wall clock time: 84 minutes 45.84 seconds (5085.84 seconds total)