Starting phenix.real_space_refine on Tue Aug 26 03:05:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0q_26263/08_2025/7u0q_26263.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0q_26263/08_2025/7u0q_26263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u0q_26263/08_2025/7u0q_26263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0q_26263/08_2025/7u0q_26263.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0q_26263/08_2025/7u0q_26263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0q_26263/08_2025/7u0q_26263.cif" } resolution = 3.86 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= -0.003 sd= 0.061 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 137 5.16 5 C 20765 2.51 5 N 5404 2.21 5 O 6415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32721 Number of models: 1 Model: "" Number of chains: 25 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: 8508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8508 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 59, 'TRANS': 1027} Chain breaks: 5 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "I" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} 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: "H" 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: "L" 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: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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 Time building chain proxies: 7.99, per 1000 atoms: 0.24 Number of scatterers: 32721 At special positions: 0 Unit cell: (164.641, 162.503, 250.169, 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 137 16.00 O 6415 8.00 N 5404 7.00 C 20765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.32 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.41 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.47 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 H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " 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 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 17 " " 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 165 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG H 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 709 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 343 " " NAG V 1 " - " ASN C 331 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7670 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 58 sheets defined 22.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.808A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.351A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.359A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 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: 3.734A 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: 4.514A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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 removed outlier: 4.115A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) 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 removed outlier: 4.408A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.709A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.587A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.101A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.565A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1033 removed outlier: 4.148A pdb=" N GLU A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.981A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1129 " --> pdb=" O CYS A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1125 through 1129' Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.057A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.768A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.621A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.501A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.784A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.391A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.575A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.642A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 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 removed outlier: 3.738A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) 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: 4.051A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.522A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.635A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.988A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.277A 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 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 1032 removed outlier: 5.061A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.604A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.348A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.589A pdb=" N ARG C 634 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.213A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.599A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.692A 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 945 through 965 removed outlier: 4.423A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.202A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 189 removed outlier: 3.777A pdb=" N HIS F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 214 No H-bonds generated for 'chain 'F' and resid 212 through 214' Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.618A pdb=" N GLY G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 189 Processing helix chain 'I' and resid 212 through 214 No H-bonds generated for 'chain 'I' and resid 212 through 214' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.625A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 191 through 195 removed outlier: 4.164A pdb=" N GLY J 194 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.651A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 67 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.921A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 131 current: chain 'A' and resid 151 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 153 current: chain 'A' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.960A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.846A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.085A 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 660 removed outlier: 5.323A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.714A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A 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 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.866A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A1086 " --> pdb=" O HIS A1083 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.932A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.363A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.014A 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: 3.875A 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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 131 current: chain 'B' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.170A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.674A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.722A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.932A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 719 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 719 current: chain 'B' and resid 1059 through 1076 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.425A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.538A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.777A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 151 through 153 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.262A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 326 removed outlier: 4.310A pdb=" N ASN C 540 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER C 325 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN C 542 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.742A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.892A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1077 removed outlier: 3.553A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.655A pdb=" N GLN F 89 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.262A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.605A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.626A pdb=" N GLY G 10 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.227A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER G 181 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER G 183 " --> pdb=" O PHE G 170 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 155 through 157 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.852A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 34 " --> pdb=" O GLN I 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.589A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.775A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU J 18 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 103 through 107 Processing sheet with id=AG3, first strand: chain 'J' and resid 124 through 128 removed outlier: 4.231A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 139 through 149 current: chain 'J' and resid 180 through 189 Processing sheet with id=AG4, first strand: chain 'J' and resid 155 through 158 removed outlier: 3.570A pdb=" N TYR J 198 " --> pdb=" O VAL J 215 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 2922 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: 8.35 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.22: 6 1.22 - 1.54: 33062 1.54 - 1.86: 401 1.86 - 2.18: 0 2.18 - 2.50: 1 Bond restraints: 33470 Sorted by residual: bond pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 1.492 2.503 -1.011 5.00e-02 4.00e+02 4.09e+02 bond pdb=" CG PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 1.503 0.900 0.603 3.40e-02 8.65e+02 3.15e+02 bond pdb=" CB ASN C 439 " pdb=" CG ASN C 439 " ideal model delta sigma weight residual 1.516 1.406 0.110 2.50e-02 1.60e+03 1.93e+01 bond pdb=" N PRO C 987 " pdb=" CA PRO C 987 " ideal model delta sigma weight residual 1.472 1.420 0.051 1.32e-02 5.74e+03 1.51e+01 bond pdb=" CD1 PHE J 67 " pdb=" CE1 PHE J 67 " ideal model delta sigma weight residual 1.382 1.270 0.112 3.00e-02 1.11e+03 1.40e+01 ... (remaining 33465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 45546 21.21 - 42.43: 1 42.43 - 63.64: 0 63.64 - 84.85: 0 84.85 - 106.06: 1 Bond angle restraints: 45548 Sorted by residual: angle pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 112.00 94.80 17.20 1.40e+00 5.10e-01 1.51e+02 angle pdb=" N PRO C 987 " pdb=" CA PRO C 987 " pdb=" CB PRO C 987 " ideal model delta sigma weight residual 103.33 90.46 12.87 1.10e+00 8.26e-01 1.37e+02 angle pdb=" CA PRO C 987 " pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 104.50 89.13 15.37 1.90e+00 2.77e-01 6.54e+01 angle pdb=" N ILE I 29 " pdb=" CA ILE I 29 " pdb=" C ILE I 29 " ideal model delta sigma weight residual 113.53 107.35 6.18 9.80e-01 1.04e+00 3.98e+01 ... (remaining 45543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 19013 22.40 - 44.80: 1292 44.80 - 67.19: 189 67.19 - 89.59: 54 89.59 - 111.99: 6 Dihedral angle restraints: 20554 sinusoidal: 8617 harmonic: 11937 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 152.32 -59.32 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CA ASP J 101 " pdb=" C ASP J 101 " pdb=" N PHE J 102 " pdb=" CA PHE J 102 " ideal model delta harmonic sigma weight residual 180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA PHE J 102 " pdb=" C PHE J 102 " pdb=" N TYR J 103 " pdb=" CA TYR J 103 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 20551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4975 0.098 - 0.197: 308 0.197 - 0.295: 11 0.295 - 0.394: 1 0.394 - 0.492: 2 Chirality restraints: 5297 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5294 not shown) Planarity restraints: 5861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " -0.115 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" CG ASN A1098 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 103 " 0.050 2.00e-02 2.50e+03 2.78e-02 1.55e+01 pdb=" CG TYR J 103 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR J 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR J 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR J 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 103 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR J 103 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 791 " -0.056 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO C 792 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 792 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 792 " -0.046 5.00e-02 4.00e+02 ... (remaining 5858 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 323 2.56 - 3.15: 26845 3.15 - 3.73: 48839 3.73 - 4.32: 65922 4.32 - 4.90: 110085 Nonbonded interactions: 252014 Sorted by model distance: nonbonded pdb=" CG GLN F 166 " pdb=" OH TYR F 173 " model vdw 1.978 3.440 nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 1.981 3.120 nonbonded pdb=" OD2 ASP C 420 " pdb=" ND2 ASN C 460 " model vdw 1.997 3.120 nonbonded pdb=" OH TYR C 421 " pdb=" O ARG C 457 " model vdw 2.000 3.040 nonbonded pdb=" O LEU B 176 " pdb=" NH2 ARG B 190 " model vdw 2.056 3.120 ... (remaining 252009 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 741 or resid 743 through 1307)) selection = (chain 'B' and (resid 14 through 542 or resid 544 through 623 or resid 633 throu \ gh 741 or resid 743 through 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 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 5.740 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.320 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 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 : 0.009 1.011 33527 Z= 0.326 Angle : 0.974 106.064 45716 Z= 0.448 Chirality : 0.049 0.492 5297 Planarity : 0.005 0.082 5823 Dihedral : 15.027 111.991 12875 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 0.08 % Allowed : 18.04 % Favored : 81.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.13), residues: 4058 helix: 1.08 (0.20), residues: 713 sheet: 0.17 (0.16), residues: 1087 loop : -1.17 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 34 TYR 0.055 0.002 TYR J 103 PHE 0.035 0.002 PHE J 67 TRP 0.031 0.002 TRP C 152 HIS 0.006 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00836 (33470) covalent geometry : angle 0.89210 (45548) SS BOND : bond 0.37283 ( 3) SS BOND : angle 31.04812 ( 6) hydrogen bonds : bond 0.22373 ( 1101) hydrogen bonds : angle 8.47124 ( 2922) link_BETA1-4 : bond 0.00316 ( 16) link_BETA1-4 : angle 2.00206 ( 48) link_NAG-ASN : bond 0.01255 ( 38) link_NAG-ASN : angle 3.11443 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 469 time to evaluate : 1.215 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8575 (pm20) cc_final: 0.8352 (pm20) REVERT: A 121 ASN cc_start: 0.7957 (m110) cc_final: 0.7334 (t0) REVERT: A 168 PHE cc_start: 0.7663 (t80) cc_final: 0.7363 (t80) REVERT: A 532 ASN cc_start: 0.8669 (t0) cc_final: 0.8397 (t0) REVERT: A 558 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8082 (tptt) REVERT: A 663 ASP cc_start: 0.8070 (t0) cc_final: 0.7714 (m-30) REVERT: A 779 GLN cc_start: 0.7894 (tp40) cc_final: 0.7640 (tp40) REVERT: A 904 TYR cc_start: 0.6767 (t80) cc_final: 0.6451 (t80) REVERT: B 129 LYS cc_start: 0.6344 (mttt) cc_final: 0.6110 (ttmt) REVERT: B 131 CYS cc_start: 0.6247 (m) cc_final: 0.5168 (m) REVERT: B 177 MET cc_start: 0.6809 (mtp) cc_final: 0.5132 (ptm) REVERT: B 198 ASP cc_start: 0.8163 (t0) cc_final: 0.7615 (t0) REVERT: B 235 ILE cc_start: 0.6947 (mm) cc_final: 0.6693 (mm) REVERT: B 614 ASP cc_start: 0.7693 (t0) cc_final: 0.7014 (t0) REVERT: B 779 GLN cc_start: 0.8053 (tt0) cc_final: 0.7769 (mt0) REVERT: B 808 ASP cc_start: 0.8083 (t0) cc_final: 0.7742 (t0) REVERT: B 816 SER cc_start: 0.8073 (p) cc_final: 0.7533 (m) REVERT: B 823 PHE cc_start: 0.7061 (t80) cc_final: 0.6779 (m-80) REVERT: B 886 TRP cc_start: 0.8930 (p90) cc_final: 0.7778 (p90) REVERT: B 904 TYR cc_start: 0.6072 (t80) cc_final: 0.5846 (t80) REVERT: B 933 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7430 (tmmt) REVERT: B 984 LEU cc_start: 0.8368 (mt) cc_final: 0.7291 (mp) REVERT: B 1017 GLU cc_start: 0.7555 (tt0) cc_final: 0.7315 (tm-30) REVERT: C 49 HIS cc_start: 0.7521 (t-90) cc_final: 0.7295 (t70) REVERT: C 128 ILE cc_start: 0.8381 (mt) cc_final: 0.7796 (mp) REVERT: C 177 MET cc_start: 0.2111 (mtp) cc_final: 0.1579 (tmm) REVERT: C 202 LYS cc_start: 0.7485 (mttt) cc_final: 0.7056 (mtpt) REVERT: C 317 ASN cc_start: 0.7555 (m-40) cc_final: 0.6770 (m-40) REVERT: C 351 TYR cc_start: 0.7532 (p90) cc_final: 0.7311 (p90) REVERT: C 377 PHE cc_start: 0.8337 (t80) cc_final: 0.8094 (t80) REVERT: C 578 ASP cc_start: 0.8277 (t0) cc_final: 0.7618 (t70) REVERT: C 586 ASP cc_start: 0.8098 (t0) cc_final: 0.7805 (m-30) REVERT: C 731 MET cc_start: 0.7999 (mtm) cc_final: 0.7687 (mtm) REVERT: C 791 THR cc_start: 0.7793 (m) cc_final: 0.7520 (p) REVERT: G 98 ASP cc_start: -0.0710 (OUTLIER) cc_final: -0.1501 (m-30) outliers start: 3 outliers final: 1 residues processed: 471 average time/residue: 0.2174 time to fit residues: 162.6639 Evaluate side-chains 278 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain G residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 314 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN I 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.217689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.195467 restraints weight = 41852.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.190795 restraints weight = 100815.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185157 restraints weight = 69224.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185566 restraints weight = 81416.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185061 restraints weight = 49483.545| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 33527 Z= 0.138 Angle : 0.672 15.650 45716 Z= 0.338 Chirality : 0.047 0.297 5297 Planarity : 0.005 0.070 5823 Dihedral : 7.243 70.916 5553 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 2.70 % Allowed : 17.07 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.36 (0.13), residues: 4058 helix: 1.30 (0.20), residues: 717 sheet: 0.29 (0.15), residues: 1147 loop : -1.06 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.030 0.002 TYR J 103 PHE 0.029 0.002 PHE C 168 TRP 0.030 0.002 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00311 (33470) covalent geometry : angle 0.65373 (45548) SS BOND : bond 0.00570 ( 3) SS BOND : angle 3.33429 ( 6) hydrogen bonds : bond 0.04763 ( 1101) hydrogen bonds : angle 6.31236 ( 2922) link_BETA1-4 : bond 0.00381 ( 16) link_BETA1-4 : angle 1.81556 ( 48) link_NAG-ASN : bond 0.00574 ( 38) link_NAG-ASN : angle 2.87733 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 294 time to evaluate : 1.300 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: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7670 (t0) cc_final: 0.7447 (m-30) REVERT: A 779 GLN cc_start: 0.7861 (tp40) cc_final: 0.7575 (mm-40) REVERT: B 276 LEU cc_start: 0.8751 (tp) cc_final: 0.8489 (tt) REVERT: B 396 TYR cc_start: 0.7663 (m-80) cc_final: 0.7309 (m-10) REVERT: B 541 PHE cc_start: 0.8946 (p90) cc_final: 0.8638 (p90) REVERT: B 614 ASP cc_start: 0.6969 (t0) cc_final: 0.6593 (t0) REVERT: B 779 GLN cc_start: 0.7838 (tt0) cc_final: 0.7619 (mt0) REVERT: B 886 TRP cc_start: 0.8725 (p90) cc_final: 0.7802 (p90) REVERT: C 153 MET cc_start: 0.2542 (pmm) cc_final: 0.2295 (pmm) REVERT: C 556 ASN cc_start: 0.8051 (m-40) cc_final: 0.7844 (m110) REVERT: C 726 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 791 THR cc_start: 0.7844 (m) cc_final: 0.7468 (p) REVERT: G 98 ASP cc_start: -0.0454 (OUTLIER) cc_final: -0.1988 (m-30) outliers start: 97 outliers final: 47 residues processed: 375 average time/residue: 0.2085 time to fit residues: 129.2304 Evaluate side-chains 292 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 217 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 215 optimal weight: 0.0370 chunk 268 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 278 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS A1088 HIS B 188 ASN B 271 GLN C 188 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS F 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.210492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.189023 restraints weight = 41940.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.184513 restraints weight = 69706.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.182195 restraints weight = 70133.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179892 restraints weight = 80004.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.177625 restraints weight = 77116.218| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 33527 Z= 0.225 Angle : 0.693 16.578 45716 Z= 0.348 Chirality : 0.048 0.291 5297 Planarity : 0.005 0.048 5823 Dihedral : 6.852 58.051 5553 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 4.55 % Allowed : 16.48 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.55 (0.13), residues: 4058 helix: 1.01 (0.19), residues: 697 sheet: 0.17 (0.15), residues: 1161 loop : -1.12 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.032 0.002 TYR C 904 PHE 0.026 0.002 PHE F 83 TRP 0.028 0.002 TRP C 353 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00543 (33470) covalent geometry : angle 0.67729 (45548) SS BOND : bond 0.00365 ( 3) SS BOND : angle 2.49971 ( 6) hydrogen bonds : bond 0.04617 ( 1101) hydrogen bonds : angle 5.95912 ( 2922) link_BETA1-4 : bond 0.00352 ( 16) link_BETA1-4 : angle 1.79024 ( 48) link_NAG-ASN : bond 0.00774 ( 38) link_NAG-ASN : angle 2.78985 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 258 time to evaluate : 1.228 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 592 PHE cc_start: 0.8609 (p90) cc_final: 0.8394 (p90) REVERT: A 726 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8684 (mt) REVERT: A 779 GLN cc_start: 0.7925 (tp40) cc_final: 0.7512 (mm-40) REVERT: A 904 TYR cc_start: 0.6896 (t80) cc_final: 0.6692 (t80) REVERT: A 1077 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7425 (p) REVERT: B 235 ILE cc_start: 0.7546 (mm) cc_final: 0.7293 (mm) REVERT: B 541 PHE cc_start: 0.8969 (p90) cc_final: 0.8729 (p90) REVERT: B 614 ASP cc_start: 0.6973 (t0) cc_final: 0.6402 (t0) REVERT: B 699 LEU cc_start: 0.7913 (mt) cc_final: 0.7590 (mt) REVERT: B 787 GLN cc_start: 0.8372 (mp10) cc_final: 0.7703 (mt0) REVERT: B 808 ASP cc_start: 0.7443 (t0) cc_final: 0.6755 (m-30) REVERT: B 886 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7944 (p90) REVERT: C 96 GLU cc_start: 0.5273 (pt0) cc_final: 0.4739 (pp20) REVERT: C 100 ILE cc_start: 0.6684 (mp) cc_final: 0.6290 (mm) REVERT: C 153 MET cc_start: 0.2556 (pmm) cc_final: 0.2347 (pmm) REVERT: C 578 ASP cc_start: 0.8087 (t0) cc_final: 0.7278 (p0) REVERT: C 791 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7538 (p) REVERT: F 104 LEU cc_start: 0.2336 (OUTLIER) cc_final: 0.2099 (tp) REVERT: G 98 ASP cc_start: -0.0284 (OUTLIER) cc_final: -0.0946 (p0) outliers start: 163 outliers final: 89 residues processed: 393 average time/residue: 0.1973 time to fit residues: 130.3869 Evaluate side-chains 320 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 225 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 134 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 330 optimal weight: 30.0000 chunk 336 optimal weight: 20.0000 chunk 358 optimal weight: 0.4980 chunk 234 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 125 ASN A 173 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1106 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.212185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190845 restraints weight = 41586.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.186472 restraints weight = 66887.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.183035 restraints weight = 60456.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.180663 restraints weight = 72292.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178208 restraints weight = 77087.743| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33527 Z= 0.147 Angle : 0.627 18.016 45716 Z= 0.312 Chirality : 0.046 0.299 5297 Planarity : 0.004 0.049 5823 Dihedral : 6.498 58.901 5553 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 3.90 % Allowed : 17.40 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.44 (0.13), residues: 4058 helix: 1.24 (0.20), residues: 699 sheet: 0.27 (0.15), residues: 1145 loop : -1.12 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.026 0.001 TYR I 49 PHE 0.019 0.001 PHE I 98 TRP 0.028 0.001 TRP C 353 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00345 (33470) covalent geometry : angle 0.61035 (45548) SS BOND : bond 0.00588 ( 3) SS BOND : angle 2.45575 ( 6) hydrogen bonds : bond 0.03984 ( 1101) hydrogen bonds : angle 5.64451 ( 2922) link_BETA1-4 : bond 0.00359 ( 16) link_BETA1-4 : angle 1.72982 ( 48) link_NAG-ASN : bond 0.00557 ( 38) link_NAG-ASN : angle 2.68068 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 253 time to evaluate : 1.291 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 779 GLN cc_start: 0.8028 (tp40) cc_final: 0.7799 (mt0) REVERT: B 52 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7457 (tt0) REVERT: B 235 ILE cc_start: 0.7504 (mm) cc_final: 0.7240 (mm) REVERT: B 614 ASP cc_start: 0.6837 (t0) cc_final: 0.6341 (t0) REVERT: B 787 GLN cc_start: 0.8274 (mp10) cc_final: 0.7634 (mt0) REVERT: B 904 TYR cc_start: 0.7161 (t80) cc_final: 0.6709 (t80) REVERT: C 100 ILE cc_start: 0.6846 (mp) cc_final: 0.6575 (mm) REVERT: C 117 LEU cc_start: 0.7316 (tp) cc_final: 0.6911 (tp) REVERT: C 177 MET cc_start: 0.2002 (ttp) cc_final: 0.1642 (tmm) REVERT: C 190 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6651 (mtp180) REVERT: C 578 ASP cc_start: 0.7986 (t0) cc_final: 0.7195 (p0) REVERT: C 726 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8513 (mm) REVERT: C 791 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7460 (p) REVERT: F 104 LEU cc_start: 0.2775 (OUTLIER) cc_final: 0.2566 (tp) REVERT: G 98 ASP cc_start: -0.0181 (OUTLIER) cc_final: -0.0651 (p0) REVERT: G 176 SER cc_start: 0.3775 (OUTLIER) cc_final: 0.3527 (t) outliers start: 140 outliers final: 89 residues processed: 373 average time/residue: 0.1988 time to fit residues: 124.2235 Evaluate side-chains 327 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 232 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 0.5980 chunk 381 optimal weight: 40.0000 chunk 378 optimal weight: 50.0000 chunk 361 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 407 optimal weight: 40.0000 chunk 268 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 360 ASN B 710 ASN B 804 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 185 ASN C 239 GLN C 314 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.204883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.187510 restraints weight = 41961.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.184428 restraints weight = 75648.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181809 restraints weight = 68226.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.178684 restraints weight = 83666.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.176849 restraints weight = 99872.030| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 33527 Z= 0.343 Angle : 0.798 16.705 45716 Z= 0.403 Chirality : 0.051 0.294 5297 Planarity : 0.005 0.052 5823 Dihedral : 6.914 59.295 5553 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 5.33 % Allowed : 17.26 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.13), residues: 4058 helix: 0.32 (0.19), residues: 702 sheet: -0.01 (0.15), residues: 1154 loop : -1.40 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 905 TYR 0.043 0.002 TYR C 904 PHE 0.035 0.003 PHE B 238 TRP 0.025 0.002 TRP C 353 HIS 0.014 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00831 (33470) covalent geometry : angle 0.78098 (45548) SS BOND : bond 0.00263 ( 3) SS BOND : angle 2.64205 ( 6) hydrogen bonds : bond 0.04990 ( 1101) hydrogen bonds : angle 6.01540 ( 2922) link_BETA1-4 : bond 0.00436 ( 16) link_BETA1-4 : angle 1.82800 ( 48) link_NAG-ASN : bond 0.00744 ( 38) link_NAG-ASN : angle 3.16362 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 253 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: A 235 ILE cc_start: 0.7526 (mm) cc_final: 0.7237 (mm) REVERT: A 284 THR cc_start: 0.8001 (m) cc_final: 0.7609 (p) REVERT: A 1077 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.7934 (p) REVERT: B 52 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 197 ILE cc_start: 0.9061 (mp) cc_final: 0.8704 (mm) REVERT: B 614 ASP cc_start: 0.7278 (t0) cc_final: 0.6400 (t0) REVERT: B 1051 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8449 (p) REVERT: C 41 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.5473 (mmtt) REVERT: C 117 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6683 (tp) REVERT: C 190 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6565 (mtp-110) REVERT: C 578 ASP cc_start: 0.8094 (t0) cc_final: 0.7385 (p0) REVERT: C 791 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7678 (p) REVERT: G 98 ASP cc_start: -0.0105 (OUTLIER) cc_final: -0.1093 (p0) outliers start: 191 outliers final: 135 residues processed: 419 average time/residue: 0.2020 time to fit residues: 142.3530 Evaluate side-chains 369 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 226 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 323 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 276 optimal weight: 0.5980 chunk 257 optimal weight: 10.0000 chunk 337 optimal weight: 40.0000 chunk 319 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 105 optimal weight: 0.5980 chunk 204 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 66 HIS ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C1010 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.209597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183402 restraints weight = 41683.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.176390 restraints weight = 60242.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173029 restraints weight = 71310.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.171361 restraints weight = 79739.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168215 restraints weight = 72886.602| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33527 Z= 0.149 Angle : 0.633 15.700 45716 Z= 0.315 Chirality : 0.046 0.292 5297 Planarity : 0.004 0.063 5823 Dihedral : 6.518 59.828 5553 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 3.71 % Allowed : 18.85 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.72 (0.13), residues: 4058 helix: 0.96 (0.20), residues: 704 sheet: 0.15 (0.16), residues: 1126 loop : -1.32 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 31 TYR 0.037 0.002 TYR I 91 PHE 0.027 0.002 PHE A 135 TRP 0.026 0.001 TRP C 353 HIS 0.015 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00350 (33470) covalent geometry : angle 0.61579 (45548) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.76804 ( 6) hydrogen bonds : bond 0.03975 ( 1101) hydrogen bonds : angle 5.58467 ( 2922) link_BETA1-4 : bond 0.00348 ( 16) link_BETA1-4 : angle 1.67213 ( 48) link_NAG-ASN : bond 0.00523 ( 38) link_NAG-ASN : angle 2.76705 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 244 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7511 (mm) cc_final: 0.7198 (mm) REVERT: A 705 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.7588 (t) REVERT: A 901 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7681 (tm130) REVERT: A 1077 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7431 (p) REVERT: B 52 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 197 ILE cc_start: 0.9117 (mp) cc_final: 0.8795 (mm) REVERT: B 616 ASN cc_start: 0.7791 (t0) cc_final: 0.7540 (m-40) REVERT: B 787 GLN cc_start: 0.8286 (mp10) cc_final: 0.7642 (mt0) REVERT: C 190 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6424 (mtp-110) REVERT: C 531 THR cc_start: 0.5917 (OUTLIER) cc_final: 0.5683 (m) REVERT: C 578 ASP cc_start: 0.8086 (t0) cc_final: 0.7312 (p0) REVERT: C 791 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7596 (p) REVERT: G 82 MET cc_start: 0.4876 (tmm) cc_final: 0.4232 (ttp) REVERT: G 98 ASP cc_start: -0.0572 (OUTLIER) cc_final: -0.0802 (p0) outliers start: 133 outliers final: 95 residues processed: 358 average time/residue: 0.2091 time to fit residues: 124.0136 Evaluate side-chains 332 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 230 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 331 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 383 optimal weight: 30.0000 chunk 334 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 61 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 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 = 0.4405 r_free = 0.4405 target = 0.207432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.191422 restraints weight = 41639.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.188381 restraints weight = 69106.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.185359 restraints weight = 57616.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.183242 restraints weight = 74879.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180870 restraints weight = 75695.476| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33527 Z= 0.189 Angle : 0.646 15.065 45716 Z= 0.323 Chirality : 0.046 0.325 5297 Planarity : 0.004 0.061 5823 Dihedral : 6.453 59.098 5553 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.90 % Rotamer: Outliers : 3.96 % Allowed : 19.05 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.72 (0.13), residues: 4058 helix: 0.99 (0.20), residues: 699 sheet: 0.12 (0.15), residues: 1133 loop : -1.32 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 31 TYR 0.030 0.002 TYR C 904 PHE 0.027 0.002 PHE B 429 TRP 0.035 0.002 TRP B 886 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00457 (33470) covalent geometry : angle 0.62985 (45548) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.85108 ( 6) hydrogen bonds : bond 0.04037 ( 1101) hydrogen bonds : angle 5.54820 ( 2922) link_BETA1-4 : bond 0.00345 ( 16) link_BETA1-4 : angle 1.67774 ( 48) link_NAG-ASN : bond 0.00556 ( 38) link_NAG-ASN : angle 2.69582 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 236 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.7580 (t) REVERT: A 901 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: A 1077 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7506 (p) REVERT: B 52 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 197 ILE cc_start: 0.8992 (mp) cc_final: 0.8671 (mm) REVERT: B 776 LYS cc_start: 0.8275 (tppt) cc_final: 0.7991 (tmtt) REVERT: B 787 GLN cc_start: 0.8263 (mp10) cc_final: 0.7563 (mt0) REVERT: B 1149 LYS cc_start: 0.4684 (OUTLIER) cc_final: 0.4109 (pttm) REVERT: C 41 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.5443 (mmtt) REVERT: C 117 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6849 (tp) REVERT: C 190 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.6168 (mtp-110) REVERT: C 531 THR cc_start: 0.6059 (OUTLIER) cc_final: 0.5693 (m) REVERT: C 578 ASP cc_start: 0.7887 (t0) cc_final: 0.7393 (p0) REVERT: C 791 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7563 (p) REVERT: F 104 LEU cc_start: 0.3021 (OUTLIER) cc_final: 0.2800 (tp) REVERT: G 82 MET cc_start: 0.4601 (tmm) cc_final: 0.4090 (ttp) REVERT: G 98 ASP cc_start: -0.0395 (OUTLIER) cc_final: -0.0755 (p0) outliers start: 142 outliers final: 113 residues processed: 361 average time/residue: 0.2081 time to fit residues: 124.7341 Evaluate side-chains 348 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 224 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 388 optimal weight: 30.0000 chunk 324 optimal weight: 20.0000 chunk 316 optimal weight: 0.6980 chunk 360 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 277 optimal weight: 0.3980 chunk 169 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 357 optimal weight: 30.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 606 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 61 ASN B 271 GLN C 164 ASN C1064 HIS ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.210798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.183393 restraints weight = 41784.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178369 restraints weight = 66097.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175491 restraints weight = 54621.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173394 restraints weight = 69089.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.171125 restraints weight = 65874.496| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33527 Z= 0.127 Angle : 0.608 15.095 45716 Z= 0.303 Chirality : 0.045 0.321 5297 Planarity : 0.004 0.060 5823 Dihedral : 6.292 58.206 5553 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 3.54 % Allowed : 19.94 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.51 (0.13), residues: 4058 helix: 1.27 (0.20), residues: 704 sheet: 0.28 (0.15), residues: 1134 loop : -1.25 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.043 0.001 TYR C 473 PHE 0.036 0.001 PHE B 429 TRP 0.032 0.002 TRP B 886 HIS 0.008 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00296 (33470) covalent geometry : angle 0.59065 (45548) SS BOND : bond 0.00307 ( 3) SS BOND : angle 1.30249 ( 6) hydrogen bonds : bond 0.03646 ( 1101) hydrogen bonds : angle 5.30770 ( 2922) link_BETA1-4 : bond 0.00357 ( 16) link_BETA1-4 : angle 1.63112 ( 48) link_NAG-ASN : bond 0.00484 ( 38) link_NAG-ASN : angle 2.79029 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 242 time to evaluate : 1.284 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 705 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.7449 (t) REVERT: A 901 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7721 (tm130) REVERT: B 52 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 197 ILE cc_start: 0.9087 (mp) cc_final: 0.8788 (mm) REVERT: B 787 GLN cc_start: 0.8316 (mp10) cc_final: 0.7589 (mt0) REVERT: B 1029 MET cc_start: 0.8869 (tpp) cc_final: 0.8568 (tpp) REVERT: B 1149 LYS cc_start: 0.4689 (OUTLIER) cc_final: 0.4154 (pttm) REVERT: C 41 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.5327 (mmtt) REVERT: C 117 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7171 (tp) REVERT: C 531 THR cc_start: 0.5947 (OUTLIER) cc_final: 0.5731 (m) REVERT: C 578 ASP cc_start: 0.8026 (t0) cc_final: 0.7373 (p0) REVERT: C 791 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7592 (p) REVERT: F 104 LEU cc_start: 0.3783 (OUTLIER) cc_final: 0.3559 (tp) REVERT: G 2 VAL cc_start: 0.2267 (t) cc_final: 0.1982 (t) REVERT: G 82 MET cc_start: 0.4661 (tmm) cc_final: 0.4092 (ttp) REVERT: G 98 ASP cc_start: -0.0418 (OUTLIER) cc_final: -0.0716 (p0) REVERT: G 174 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4120 (pp) outliers start: 127 outliers final: 97 residues processed: 351 average time/residue: 0.2087 time to fit residues: 121.5621 Evaluate side-chains 327 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 220 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 264 optimal weight: 8.9990 chunk 261 optimal weight: 40.0000 chunk 162 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 373 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 340 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 138 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 271 GLN B 762 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.209735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.183887 restraints weight = 41450.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.178451 restraints weight = 60621.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.174852 restraints weight = 51854.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171942 restraints weight = 61097.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169236 restraints weight = 61868.103| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33527 Z= 0.153 Angle : 0.618 14.580 45716 Z= 0.309 Chirality : 0.046 0.322 5297 Planarity : 0.004 0.058 5823 Dihedral : 6.278 58.856 5553 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 3.76 % Allowed : 19.83 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.49 (0.13), residues: 4058 helix: 1.27 (0.20), residues: 699 sheet: 0.32 (0.16), residues: 1141 loop : -1.24 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 31 TYR 0.037 0.002 TYR C 473 PHE 0.024 0.002 PHE A 168 TRP 0.030 0.002 TRP C 353 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00367 (33470) covalent geometry : angle 0.60272 (45548) SS BOND : bond 0.00187 ( 3) SS BOND : angle 1.72521 ( 6) hydrogen bonds : bond 0.03715 ( 1101) hydrogen bonds : angle 5.27436 ( 2922) link_BETA1-4 : bond 0.00353 ( 16) link_BETA1-4 : angle 1.65253 ( 48) link_NAG-ASN : bond 0.00497 ( 38) link_NAG-ASN : angle 2.63598 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 231 time to evaluate : 1.389 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 235 ILE cc_start: 0.7337 (mm) cc_final: 0.6992 (mm) REVERT: B 52 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 197 ILE cc_start: 0.9101 (mp) cc_final: 0.8791 (mm) REVERT: B 787 GLN cc_start: 0.8354 (mp10) cc_final: 0.7562 (mt0) REVERT: B 1149 LYS cc_start: 0.4521 (OUTLIER) cc_final: 0.4024 (pttm) REVERT: C 41 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.5344 (mmtt) REVERT: C 117 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7167 (tp) REVERT: C 190 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6132 (mtp-110) REVERT: C 531 THR cc_start: 0.6044 (OUTLIER) cc_final: 0.5785 (m) REVERT: C 578 ASP cc_start: 0.8013 (t0) cc_final: 0.7362 (p0) REVERT: C 981 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6347 (pp) REVERT: G 2 VAL cc_start: 0.2337 (t) cc_final: 0.2029 (t) REVERT: G 82 MET cc_start: 0.4647 (tmm) cc_final: 0.4117 (ttp) REVERT: G 174 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4113 (pp) outliers start: 135 outliers final: 108 residues processed: 348 average time/residue: 0.1993 time to fit residues: 116.0888 Evaluate side-chains 333 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 218 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 44 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 955 ASN A1135 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.204269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188121 restraints weight = 42167.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.184257 restraints weight = 71026.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.181659 restraints weight = 71346.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179336 restraints weight = 84068.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.177867 restraints weight = 89609.177| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 33527 Z= 0.347 Angle : 0.776 14.122 45716 Z= 0.394 Chirality : 0.051 0.331 5297 Planarity : 0.005 0.061 5823 Dihedral : 6.658 59.448 5551 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.84 % Favored : 94.14 % Rotamer: Outliers : 3.63 % Allowed : 20.16 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.92 (0.13), residues: 4058 helix: 0.52 (0.19), residues: 702 sheet: 0.11 (0.16), residues: 1134 loop : -1.41 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 31 TYR 0.043 0.002 TYR C 904 PHE 0.034 0.003 PHE B 429 TRP 0.028 0.002 TRP C 353 HIS 0.012 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00848 (33470) covalent geometry : angle 0.76167 (45548) SS BOND : bond 0.00234 ( 3) SS BOND : angle 1.97148 ( 6) hydrogen bonds : bond 0.04657 ( 1101) hydrogen bonds : angle 5.69387 ( 2922) link_BETA1-4 : bond 0.00454 ( 16) link_BETA1-4 : angle 1.81161 ( 48) link_NAG-ASN : bond 0.00686 ( 38) link_NAG-ASN : angle 2.88388 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 228 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7492 (mm) cc_final: 0.7240 (mm) REVERT: A 901 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7783 (tm130) REVERT: B 52 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 102 ARG cc_start: 0.6983 (mmt180) cc_final: 0.6584 (mmt90) REVERT: B 197 ILE cc_start: 0.9035 (mp) cc_final: 0.8666 (mm) REVERT: B 787 GLN cc_start: 0.8344 (mp10) cc_final: 0.7612 (mt0) REVERT: B 1149 LYS cc_start: 0.4521 (OUTLIER) cc_final: 0.4003 (pttm) REVERT: C 41 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.5514 (mmtt) REVERT: C 190 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6161 (mtp-110) REVERT: C 578 ASP cc_start: 0.7960 (t0) cc_final: 0.7444 (p0) REVERT: G 2 VAL cc_start: 0.2621 (t) cc_final: 0.2305 (t) REVERT: G 82 MET cc_start: 0.3863 (tmm) cc_final: 0.3290 (ttp) outliers start: 130 outliers final: 114 residues processed: 341 average time/residue: 0.2037 time to fit residues: 116.1818 Evaluate side-chains 336 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 218 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 44 optimal weight: 0.0670 chunk 306 optimal weight: 0.9980 chunk 338 optimal weight: 20.0000 chunk 398 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 chunk 278 optimal weight: 0.4980 chunk 295 optimal weight: 0.6980 chunk 182 optimal weight: 0.4980 chunk 405 optimal weight: 50.0000 chunk 244 optimal weight: 0.2980 chunk 329 optimal weight: 20.0000 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.210780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.185000 restraints weight = 41978.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.178750 restraints weight = 61059.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.174903 restraints weight = 62158.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173271 restraints weight = 69454.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171070 restraints weight = 59443.593| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33527 Z= 0.117 Angle : 0.615 14.851 45716 Z= 0.306 Chirality : 0.045 0.325 5297 Planarity : 0.004 0.064 5823 Dihedral : 6.258 56.984 5551 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.70 % Favored : 96.28 % Rotamer: Outliers : 2.82 % Allowed : 20.86 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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 aren not related in a simple way. whole: -0.51 (0.13), residues: 4058 helix: 1.24 (0.20), residues: 697 sheet: 0.32 (0.16), residues: 1111 loop : -1.23 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 408 TYR 0.034 0.002 TYR C 473 PHE 0.049 0.001 PHE B 429 TRP 0.034 0.002 TRP B 886 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00266 (33470) covalent geometry : angle 0.60099 (45548) SS BOND : bond 0.00192 ( 3) SS BOND : angle 1.37191 ( 6) hydrogen bonds : bond 0.03652 ( 1101) hydrogen bonds : angle 5.24427 ( 2922) link_BETA1-4 : bond 0.00375 ( 16) link_BETA1-4 : angle 1.62849 ( 48) link_NAG-ASN : bond 0.00475 ( 38) link_NAG-ASN : angle 2.48305 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4881.18 seconds wall clock time: 86 minutes 21.22 seconds (5181.22 seconds total)