Starting phenix.real_space_refine on Fri Mar 6 07:07:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fem_31557/03_2026/7fem_31557.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fem_31557/03_2026/7fem_31557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fem_31557/03_2026/7fem_31557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fem_31557/03_2026/7fem_31557.map" model { file = "/net/cci-nas-00/data/ceres_data/7fem_31557/03_2026/7fem_31557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fem_31557/03_2026/7fem_31557.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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 133 5.16 5 C 18471 2.51 5 N 4731 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28977 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7782 Classifications: {'peptide': 997} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7814 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 50, 'TRANS': 950} Chain breaks: 7 Chain: "C" Number of atoms: 7831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7831 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 50, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4724 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 23, 'TRANS': 554} Chain breaks: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "I" 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: "J" 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: "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: "A" 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: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" 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 Time building chain proxies: 6.46, per 1000 atoms: 0.22 Number of scatterers: 28977 At special positions: 0 Unit cell: (148.24, 130.56, 238, 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 133 16.00 O 5642 8.00 N 4731 7.00 C 18471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 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 V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C1134 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 709 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG V 1 " - " ASN A 709 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6712 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 43 sheets defined 30.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.111A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.666A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.769A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.896A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 932 removed outlier: 6.574A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 4.229A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.620A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.545A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1035 removed outlier: 5.081A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.924A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.741A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.569A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.579A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 898 through 907 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.006A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.167A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1033 removed outlier: 5.169A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.299A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.588A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.506A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.878A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.677A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.072A 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: 3.745A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.881A 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 removed outlier: 3.730A pdb=" N ALA C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.951A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C1015 " --> pdb=" O GLN C1011 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.027A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 92 through 101 removed outlier: 5.154A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 removed outlier: 3.914A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.296A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.590A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 4.844A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.699A pdb=" N GLY D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 226 through 248 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.857A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 282 " --> pdb=" O TYR D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 307 through 319 Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.691A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.593A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.690A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 4.334A pdb=" N THR D 453 " --> pdb=" O THR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 485 removed outlier: 3.812A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.175A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 4.244A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.769A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 587 removed outlier: 4.018A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.671A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.559A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 94 removed outlier: 4.033A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.922A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.795A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 540 Processing sheet with id=AB1, first strand: chain 'A' and resid 673 through 675 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.640A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.539A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.562A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 171 removed outlier: 3.926A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 318 removed outlier: 7.237A pdb=" N VAL B 597 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 317 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 595 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.948A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 357 removed outlier: 4.456A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 554 removed outlier: 6.481A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.643A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.208A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.590A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.841A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.293A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.188A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.661A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 664 through 667 removed outlier: 5.798A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.765A pdb=" N GLN C1071 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.765A pdb=" N GLN C1071 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.819A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'D' and resid 349 through 352 removed outlier: 5.654A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.26 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.54: 29146 1.54 - 1.87: 486 1.87 - 2.20: 2 2.20 - 2.53: 0 2.53 - 2.86: 1 Bond restraints: 29635 Sorted by residual: bond pdb=" CB ASN D 437 " pdb=" CG ASN D 437 " ideal model delta sigma weight residual 1.516 2.858 -1.342 2.50e-02 1.60e+03 2.88e+03 bond pdb=" CD1 TYR D 279 " pdb=" CE1 TYR D 279 " ideal model delta sigma weight residual 1.382 2.131 -0.749 3.00e-02 1.11e+03 6.23e+02 bond pdb=" CD2 TYR D 279 " pdb=" CE2 TYR D 279 " ideal model delta sigma weight residual 1.382 2.084 -0.702 3.00e-02 1.11e+03 5.48e+02 bond pdb=" CE2 TYR D 279 " pdb=" CZ TYR D 279 " ideal model delta sigma weight residual 1.378 1.805 -0.427 2.40e-02 1.74e+03 3.16e+02 bond pdb=" CE1 TYR D 279 " pdb=" CZ TYR D 279 " ideal model delta sigma weight residual 1.378 1.781 -0.403 2.40e-02 1.74e+03 2.83e+02 ... (remaining 29630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 38313 2.27 - 4.55: 1722 4.55 - 6.82: 219 6.82 - 9.10: 35 9.10 - 11.37: 16 Bond angle restraints: 40305 Sorted by residual: angle pdb=" CA ASN D 437 " pdb=" CB ASN D 437 " pdb=" CG ASN D 437 " ideal model delta sigma weight residual 112.60 123.38 -10.78 1.00e+00 1.00e+00 1.16e+02 angle pdb=" OD1 ASN D 437 " pdb=" CG ASN D 437 " pdb=" ND2 ASN D 437 " ideal model delta sigma weight residual 122.60 115.03 7.57 1.00e+00 1.00e+00 5.73e+01 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.49 110.48 10.01 1.38e+00 5.25e-01 5.26e+01 angle pdb=" N ILE A 896 " pdb=" CA ILE A 896 " pdb=" C ILE A 896 " ideal model delta sigma weight residual 109.19 103.80 5.39 8.20e-01 1.49e+00 4.33e+01 angle pdb=" C TRP D 477 " pdb=" N TRP D 478 " pdb=" CA TRP D 478 " ideal model delta sigma weight residual 121.90 114.21 7.69 1.26e+00 6.30e-01 3.72e+01 ... (remaining 40300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 17124 22.28 - 44.56: 1015 44.56 - 66.84: 202 66.84 - 89.12: 36 89.12 - 111.40: 12 Dihedral angle restraints: 18389 sinusoidal: 7966 harmonic: 10423 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.73 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 12.25 80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 172.74 -79.74 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 18386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4494 0.118 - 0.236: 194 0.236 - 0.354: 8 0.354 - 0.472: 5 0.472 - 0.590: 4 Chirality restraints: 4705 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" CB THR D 445 " pdb=" CA THR D 445 " pdb=" OG1 THR D 445 " pdb=" CG2 THR D 445 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4702 not shown) Planarity restraints: 5175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " -0.033 2.00e-02 2.50e+03 3.53e-02 3.11e+01 pdb=" CG TRP D 461 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 279 " -0.039 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR D 279 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 279 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 279 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR D 279 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 279 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 279 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR D 279 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 441 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LYS D 441 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS D 441 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN D 442 " 0.023 2.00e-02 2.50e+03 ... (remaining 5172 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 480 2.59 - 3.16: 26579 3.16 - 3.74: 42400 3.74 - 4.32: 59171 4.32 - 4.90: 93280 Nonbonded interactions: 221910 Sorted by model distance: nonbonded pdb=" OG SER C 813 " pdb=" OE1 GLU C 868 " model vdw 2.008 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" NZ LYS B 195 " model vdw 2.091 3.120 nonbonded pdb=" OG SER B 375 " pdb=" O ALA B 435 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.093 3.040 nonbonded pdb=" ND2 ASN B 394 " pdb=" OH TYR C 200 " model vdw 2.113 3.120 ... (remaining 221905 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' selection = (chain 'B' and (resid 27 through 68 or resid 81 through 165 or (resid 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 243 or r \ esid 264 through 1307)) selection = (chain 'C' and (resid 27 through 68 or resid 81 through 165 or (resid 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 172 or r \ esid 187 through 243 or resid 264 through 621 or resid 641 through 1307)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' } 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=0.00 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.820 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.342 29736 Z= 0.557 Angle : 1.132 18.746 40564 Z= 0.636 Chirality : 0.061 0.590 4705 Planarity : 0.007 0.097 5132 Dihedral : 14.634 111.401 11554 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.01 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.12), residues: 3523 helix: -1.95 (0.14), residues: 983 sheet: -2.01 (0.20), residues: 573 loop : -3.18 (0.12), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 306 TYR 0.046 0.002 TYR D 279 PHE 0.035 0.003 PHE C 888 TRP 0.095 0.004 TRP D 461 HIS 0.012 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.01351 (29635) covalent geometry : angle 1.08594 (40305) SS BOND : bond 0.00697 ( 41) SS BOND : angle 2.88100 ( 82) hydrogen bonds : bond 0.16541 ( 1037) hydrogen bonds : angle 8.81866 ( 2913) Misc. bond : bond 0.00047 ( 1) link_BETA1-4 : bond 0.00790 ( 16) link_BETA1-4 : angle 3.36251 ( 48) link_NAG-ASN : bond 0.00889 ( 43) link_NAG-ASN : angle 4.97925 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8596 (ptt-90) cc_final: 0.8095 (ttp80) REVERT: A 776 LYS cc_start: 0.8610 (tttt) cc_final: 0.8345 (tppp) REVERT: B 118 LEU cc_start: 0.9335 (tp) cc_final: 0.8533 (pp) REVERT: B 740 MET cc_start: 0.8412 (mmt) cc_final: 0.8171 (tpp) REVERT: B 763 LEU cc_start: 0.9509 (mt) cc_final: 0.9293 (mp) REVERT: B 1030 SER cc_start: 0.9200 (p) cc_final: 0.8446 (p) REVERT: D 366 MET cc_start: 0.9224 (mpp) cc_final: 0.8843 (mmt) REVERT: D 376 MET cc_start: 0.7000 (mtm) cc_final: 0.6695 (ttm) REVERT: D 557 MET cc_start: 0.8383 (tmm) cc_final: 0.7849 (mmt) REVERT: D 611 SER cc_start: 0.8817 (p) cc_final: 0.7238 (t) REVERT: D 613 TYR cc_start: 0.2994 (p90) cc_final: 0.2723 (t80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1821 time to fit residues: 50.2445 Evaluate side-chains 88 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 544 ASN B 317 ASN B 644 GLN B 856 ASN B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1005 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.082522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054849 restraints weight = 154262.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056312 restraints weight = 94664.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056381 restraints weight = 55183.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056532 restraints weight = 48348.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056755 restraints weight = 47008.556| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.331 29736 Z= 0.465 Angle : 0.809 18.023 40564 Z= 0.416 Chirality : 0.051 0.478 4705 Planarity : 0.006 0.071 5132 Dihedral : 10.199 106.563 5064 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.83 % Favored : 92.08 % Rotamer: Outliers : 0.35 % Allowed : 6.58 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.13), residues: 3523 helix: -0.94 (0.16), residues: 980 sheet: -1.63 (0.20), residues: 598 loop : -2.76 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.034 0.002 TYR D 279 PHE 0.030 0.002 PHE D 315 TRP 0.045 0.002 TRP D 461 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.01169 (29635) covalent geometry : angle 0.77660 (40305) SS BOND : bond 0.00501 ( 41) SS BOND : angle 2.00745 ( 82) hydrogen bonds : bond 0.05508 ( 1037) hydrogen bonds : angle 6.89730 ( 2913) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00566 ( 16) link_BETA1-4 : angle 2.53563 ( 48) link_NAG-ASN : bond 0.00572 ( 43) link_NAG-ASN : angle 3.50047 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.7448 (ttm) cc_final: 0.7150 (ttm) REVERT: B 118 LEU cc_start: 0.9517 (tp) cc_final: 0.8845 (pp) REVERT: B 353 TRP cc_start: 0.7457 (p-90) cc_final: 0.7256 (p-90) REVERT: B 731 MET cc_start: 0.9136 (ptp) cc_final: 0.8866 (ptm) REVERT: B 740 MET cc_start: 0.8944 (mmt) cc_final: 0.8646 (tpp) REVERT: B 763 LEU cc_start: 0.9598 (mt) cc_final: 0.9347 (mp) REVERT: C 900 MET cc_start: 0.9225 (mmp) cc_final: 0.8759 (mmt) REVERT: C 964 LYS cc_start: 0.9371 (ttmm) cc_final: 0.9114 (mtmm) REVERT: C 1029 MET cc_start: 0.9032 (tpp) cc_final: 0.8196 (tpp) REVERT: D 82 MET cc_start: 0.7498 (ptp) cc_final: 0.7110 (ppp) REVERT: D 323 MET cc_start: 0.5918 (tpt) cc_final: 0.5664 (tpp) REVERT: D 360 MET cc_start: 0.7373 (mmm) cc_final: 0.6301 (mmt) REVERT: D 366 MET cc_start: 0.9086 (mpp) cc_final: 0.8825 (mmt) REVERT: D 557 MET cc_start: 0.8537 (tmm) cc_final: 0.7845 (mmt) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.1732 time to fit residues: 38.5741 Evaluate side-chains 91 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 355 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 328 optimal weight: 20.0000 chunk 113 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 913 GLN A 953 ASN B 52 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 96 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** 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 = 0.3789 r_free = 0.3789 target = 0.083377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054700 restraints weight = 152443.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056088 restraints weight = 79061.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057011 restraints weight = 52556.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057626 restraints weight = 40820.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057942 restraints weight = 34939.466| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.333 29736 Z= 0.442 Angle : 0.736 18.097 40564 Z= 0.377 Chirality : 0.049 0.442 4705 Planarity : 0.005 0.069 5132 Dihedral : 9.357 105.666 5064 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.84 % Favored : 93.07 % Rotamer: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.13), residues: 3523 helix: -0.49 (0.16), residues: 991 sheet: -1.35 (0.20), residues: 594 loop : -2.51 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 514 TYR 0.028 0.001 TYR D 279 PHE 0.021 0.002 PHE B 906 TRP 0.025 0.002 TRP D 461 HIS 0.007 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01126 (29635) covalent geometry : angle 0.70439 (40305) SS BOND : bond 0.00415 ( 41) SS BOND : angle 1.83395 ( 82) hydrogen bonds : bond 0.04946 ( 1037) hydrogen bonds : angle 6.43054 ( 2913) Misc. bond : bond 0.00023 ( 1) link_BETA1-4 : bond 0.00539 ( 16) link_BETA1-4 : angle 2.37134 ( 48) link_NAG-ASN : bond 0.00536 ( 43) link_NAG-ASN : angle 3.30285 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 TYR cc_start: 0.9227 (m-10) cc_final: 0.8420 (m-80) REVERT: B 731 MET cc_start: 0.9200 (ptp) cc_final: 0.8914 (ptm) REVERT: B 763 LEU cc_start: 0.9537 (mt) cc_final: 0.9270 (mp) REVERT: C 900 MET cc_start: 0.9293 (mmp) cc_final: 0.8956 (mmt) REVERT: C 1029 MET cc_start: 0.9003 (tpp) cc_final: 0.8792 (tpp) REVERT: D 82 MET cc_start: 0.7689 (ptp) cc_final: 0.7018 (ppp) REVERT: D 366 MET cc_start: 0.9089 (mpp) cc_final: 0.8826 (mmt) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.1737 time to fit residues: 34.8541 Evaluate side-chains 83 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 229 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 155 optimal weight: 0.0870 chunk 341 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 762 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.082166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057491 restraints weight = 159138.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056463 restraints weight = 110903.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056994 restraints weight = 85142.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057115 restraints weight = 75522.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057311 restraints weight = 65656.803| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.333 29736 Z= 0.472 Angle : 0.761 17.771 40564 Z= 0.386 Chirality : 0.049 0.452 4705 Planarity : 0.005 0.068 5132 Dihedral : 8.897 103.209 5064 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 0.16 % Allowed : 4.28 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.13), residues: 3523 helix: -0.45 (0.16), residues: 1004 sheet: -1.25 (0.20), residues: 622 loop : -2.41 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 177 TYR 0.026 0.002 TYR D 279 PHE 0.017 0.002 PHE B 906 TRP 0.024 0.002 TRP D 275 HIS 0.011 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01184 (29635) covalent geometry : angle 0.72876 (40305) SS BOND : bond 0.00459 ( 41) SS BOND : angle 1.99117 ( 82) hydrogen bonds : bond 0.04935 ( 1037) hydrogen bonds : angle 6.31913 ( 2913) Misc. bond : bond 0.00024 ( 1) link_BETA1-4 : bond 0.00535 ( 16) link_BETA1-4 : angle 2.39975 ( 48) link_NAG-ASN : bond 0.00618 ( 43) link_NAG-ASN : angle 3.38667 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.7468 (ptp) cc_final: 0.7234 (ptp) REVERT: B 697 MET cc_start: 0.8443 (ttp) cc_final: 0.8078 (ttt) REVERT: B 731 MET cc_start: 0.9236 (ptp) cc_final: 0.8973 (ptm) REVERT: B 763 LEU cc_start: 0.9541 (mt) cc_final: 0.9330 (mp) REVERT: C 900 MET cc_start: 0.9053 (mmp) cc_final: 0.8651 (mmt) REVERT: C 1029 MET cc_start: 0.8921 (tpp) cc_final: 0.8685 (tpp) REVERT: D 360 MET cc_start: 0.6951 (mmm) cc_final: 0.6734 (mmm) REVERT: D 366 MET cc_start: 0.9127 (mpp) cc_final: 0.8846 (mmt) REVERT: D 582 ARG cc_start: 0.9227 (tpm170) cc_final: 0.8621 (ppt170) outliers start: 5 outliers final: 2 residues processed: 109 average time/residue: 0.1756 time to fit residues: 32.5563 Evaluate side-chains 80 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 162 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 233 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 chunk 204 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 33 optimal weight: 50.0000 chunk 59 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1002 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.083456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059057 restraints weight = 158747.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058753 restraints weight = 113824.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.058459 restraints weight = 93339.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058867 restraints weight = 83497.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059016 restraints weight = 67991.583| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.348 29736 Z= 0.438 Angle : 0.691 18.231 40564 Z= 0.352 Chirality : 0.048 0.453 4705 Planarity : 0.005 0.070 5132 Dihedral : 8.327 101.876 5064 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.98 % Rotamer: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.03 (0.14), residues: 3523 helix: -0.04 (0.17), residues: 990 sheet: -1.05 (0.20), residues: 629 loop : -2.24 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 514 TYR 0.033 0.001 TYR D 279 PHE 0.028 0.001 PHE A 823 TRP 0.041 0.002 TRP D 478 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.01119 (29635) covalent geometry : angle 0.65981 (40305) SS BOND : bond 0.00433 ( 41) SS BOND : angle 1.80172 ( 82) hydrogen bonds : bond 0.04367 ( 1037) hydrogen bonds : angle 5.94034 ( 2913) Misc. bond : bond 0.00025 ( 1) link_BETA1-4 : bond 0.00525 ( 16) link_BETA1-4 : angle 2.29520 ( 48) link_NAG-ASN : bond 0.00506 ( 43) link_NAG-ASN : angle 3.15065 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 697 MET cc_start: 0.8280 (ttp) cc_final: 0.8018 (ttt) REVERT: B 731 MET cc_start: 0.9039 (ptp) cc_final: 0.8802 (ptm) REVERT: C 515 PHE cc_start: 0.7619 (m-10) cc_final: 0.7371 (m-80) REVERT: C 900 MET cc_start: 0.8844 (mmp) cc_final: 0.8509 (mmt) REVERT: C 1029 MET cc_start: 0.8827 (tpp) cc_final: 0.8101 (tmm) REVERT: D 270 MET cc_start: 0.5421 (ptm) cc_final: 0.5189 (tmm) REVERT: D 323 MET cc_start: 0.6363 (tpt) cc_final: 0.6152 (tpp) REVERT: D 366 MET cc_start: 0.9165 (mpp) cc_final: 0.8847 (mmt) REVERT: D 582 ARG cc_start: 0.9243 (tpm170) cc_final: 0.8578 (ppt170) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 0.1777 time to fit residues: 33.6442 Evaluate side-chains 84 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 125 optimal weight: 0.6980 chunk 265 optimal weight: 0.0070 chunk 294 optimal weight: 0.1980 chunk 255 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 762 GLN B1083 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** 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 = 0.3811 r_free = 0.3811 target = 0.083464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059080 restraints weight = 158762.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058814 restraints weight = 115534.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058818 restraints weight = 86136.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059011 restraints weight = 79703.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.059661 restraints weight = 67190.286| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.335 29736 Z= 0.436 Angle : 0.666 17.904 40564 Z= 0.339 Chirality : 0.047 0.446 4705 Planarity : 0.004 0.070 5132 Dihedral : 7.954 101.429 5064 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.84 (0.14), residues: 3523 helix: 0.16 (0.17), residues: 978 sheet: -1.00 (0.20), residues: 652 loop : -2.12 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.033 0.001 TYR D 279 PHE 0.025 0.001 PHE B 377 TRP 0.016 0.001 TRP D 275 HIS 0.006 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01113 (29635) covalent geometry : angle 0.63700 (40305) SS BOND : bond 0.00390 ( 41) SS BOND : angle 1.67571 ( 82) hydrogen bonds : bond 0.04223 ( 1037) hydrogen bonds : angle 5.82026 ( 2913) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00500 ( 16) link_BETA1-4 : angle 2.19054 ( 48) link_NAG-ASN : bond 0.00510 ( 43) link_NAG-ASN : angle 3.04191 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 THR cc_start: 0.8140 (m) cc_final: 0.7804 (p) REVERT: B 392 PHE cc_start: 0.7925 (m-80) cc_final: 0.7647 (m-10) REVERT: B 697 MET cc_start: 0.8200 (ttp) cc_final: 0.7919 (ttt) REVERT: C 900 MET cc_start: 0.8830 (mmp) cc_final: 0.8476 (mmt) REVERT: C 1029 MET cc_start: 0.8623 (tpp) cc_final: 0.8007 (tmm) REVERT: D 62 MET cc_start: 0.8944 (ptp) cc_final: 0.8728 (ptp) REVERT: D 323 MET cc_start: 0.6376 (tpt) cc_final: 0.6107 (tpp) REVERT: D 366 MET cc_start: 0.9200 (mpp) cc_final: 0.8937 (mmt) REVERT: D 376 MET cc_start: 0.5853 (ptt) cc_final: 0.4942 (ttp) REVERT: D 582 ARG cc_start: 0.9247 (tpm170) cc_final: 0.8598 (ppt170) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1773 time to fit residues: 35.4761 Evaluate side-chains 83 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 327 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 182 optimal weight: 0.0670 chunk 303 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 764 ASN A 777 ASN C 239 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 442 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.083447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056813 restraints weight = 165560.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058480 restraints weight = 103904.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.058234 restraints weight = 63166.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.058518 restraints weight = 60145.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.058574 restraints weight = 55920.177| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.337 29736 Z= 0.450 Angle : 0.695 17.631 40564 Z= 0.354 Chirality : 0.047 0.456 4705 Planarity : 0.005 0.069 5132 Dihedral : 7.755 101.170 5064 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.14), residues: 3523 helix: 0.12 (0.17), residues: 987 sheet: -0.92 (0.20), residues: 654 loop : -2.12 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 161 TYR 0.032 0.001 TYR D 279 PHE 0.017 0.001 PHE A 823 TRP 0.024 0.002 TRP D 168 HIS 0.007 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.01141 (29635) covalent geometry : angle 0.66605 (40305) SS BOND : bond 0.00374 ( 41) SS BOND : angle 1.86754 ( 82) hydrogen bonds : bond 0.04383 ( 1037) hydrogen bonds : angle 5.81687 ( 2913) Misc. bond : bond 0.00020 ( 1) link_BETA1-4 : bond 0.00529 ( 16) link_BETA1-4 : angle 2.19679 ( 48) link_NAG-ASN : bond 0.00544 ( 43) link_NAG-ASN : angle 3.05327 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9121 (ptp) cc_final: 0.8902 (ptp) REVERT: A 902 MET cc_start: 0.9210 (mmm) cc_final: 0.8973 (tpp) REVERT: B 392 PHE cc_start: 0.8054 (m-80) cc_final: 0.7821 (m-10) REVERT: C 900 MET cc_start: 0.9091 (mmp) cc_final: 0.8732 (mmt) REVERT: C 1029 MET cc_start: 0.8710 (tpp) cc_final: 0.8177 (tmm) REVERT: D 62 MET cc_start: 0.9061 (ptp) cc_final: 0.8772 (ptp) REVERT: D 323 MET cc_start: 0.6610 (tpt) cc_final: 0.6237 (tpp) REVERT: D 360 MET cc_start: 0.6958 (mmm) cc_final: 0.6399 (mmt) REVERT: D 366 MET cc_start: 0.9222 (mpp) cc_final: 0.8983 (mmt) REVERT: D 376 MET cc_start: 0.6497 (ptt) cc_final: 0.5861 (ttp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1691 time to fit residues: 31.0242 Evaluate side-chains 80 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 182 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 341 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.083259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058590 restraints weight = 158221.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.058171 restraints weight = 103525.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.058108 restraints weight = 85249.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058280 restraints weight = 85635.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058477 restraints weight = 69577.199| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.334 29736 Z= 0.434 Angle : 0.667 17.778 40564 Z= 0.338 Chirality : 0.047 0.460 4705 Planarity : 0.004 0.070 5132 Dihedral : 7.582 101.374 5064 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3523 helix: 0.34 (0.17), residues: 981 sheet: -0.89 (0.19), residues: 653 loop : -2.03 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 161 TYR 0.031 0.001 TYR D 279 PHE 0.024 0.001 PHE C 490 TRP 0.019 0.001 TRP D 168 HIS 0.007 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.01110 (29635) covalent geometry : angle 0.63850 (40305) SS BOND : bond 0.00438 ( 41) SS BOND : angle 1.74399 ( 82) hydrogen bonds : bond 0.04091 ( 1037) hydrogen bonds : angle 5.68085 ( 2913) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.00583 ( 16) link_BETA1-4 : angle 2.12946 ( 48) link_NAG-ASN : bond 0.00485 ( 43) link_NAG-ASN : angle 2.95661 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9020 (ptp) cc_final: 0.8721 (ptp) REVERT: B 376 THR cc_start: 0.8104 (m) cc_final: 0.7775 (p) REVERT: C 900 MET cc_start: 0.9191 (mmp) cc_final: 0.8840 (mmt) REVERT: C 1029 MET cc_start: 0.8682 (tpp) cc_final: 0.8044 (tmm) REVERT: D 360 MET cc_start: 0.7101 (mmm) cc_final: 0.6536 (mmt) REVERT: D 376 MET cc_start: 0.6438 (ptt) cc_final: 0.5708 (ttp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1642 time to fit residues: 31.0072 Evaluate side-chains 79 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 317 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 345 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 287 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 373 HIS ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** 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 = 0.3805 r_free = 0.3805 target = 0.083249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055704 restraints weight = 158045.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056962 restraints weight = 88144.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057769 restraints weight = 60791.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.058314 restraints weight = 47984.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058607 restraints weight = 41594.368| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.334 29736 Z= 0.435 Angle : 0.676 17.479 40564 Z= 0.342 Chirality : 0.047 0.467 4705 Planarity : 0.004 0.069 5132 Dihedral : 7.411 100.749 5064 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.59 (0.14), residues: 3523 helix: 0.40 (0.17), residues: 980 sheet: -0.88 (0.19), residues: 650 loop : -1.97 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 161 TYR 0.030 0.001 TYR D 279 PHE 0.021 0.001 PHE C 490 TRP 0.026 0.002 TRP A 886 HIS 0.008 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.01112 (29635) covalent geometry : angle 0.64601 (40305) SS BOND : bond 0.00369 ( 41) SS BOND : angle 1.71411 ( 82) hydrogen bonds : bond 0.04113 ( 1037) hydrogen bonds : angle 5.65881 ( 2913) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00540 ( 16) link_BETA1-4 : angle 2.10543 ( 48) link_NAG-ASN : bond 0.00540 ( 43) link_NAG-ASN : angle 3.12121 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9120 (ptp) cc_final: 0.8796 (ptp) REVERT: B 376 THR cc_start: 0.8045 (m) cc_final: 0.7733 (p) REVERT: C 900 MET cc_start: 0.9154 (mmp) cc_final: 0.8848 (mmt) REVERT: C 1029 MET cc_start: 0.8782 (tpp) cc_final: 0.8131 (tmm) REVERT: D 62 MET cc_start: 0.9119 (ptp) cc_final: 0.8908 (ptp) REVERT: D 82 MET cc_start: 0.7127 (ppp) cc_final: 0.6916 (ppp) REVERT: D 323 MET cc_start: 0.6237 (tpt) cc_final: 0.5841 (tpp) REVERT: D 360 MET cc_start: 0.7121 (mmm) cc_final: 0.6551 (mmt) REVERT: D 582 ARG cc_start: 0.8655 (tpm170) cc_final: 0.8316 (ppt170) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1663 time to fit residues: 30.3279 Evaluate side-chains 79 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 235 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN C 544 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.081655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056306 restraints weight = 159152.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056236 restraints weight = 114620.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056127 restraints weight = 83837.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056422 restraints weight = 81932.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056548 restraints weight = 68076.039| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.335 29736 Z= 0.466 Angle : 0.738 17.016 40564 Z= 0.372 Chirality : 0.048 0.479 4705 Planarity : 0.005 0.068 5132 Dihedral : 7.522 101.325 5064 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.38 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.76 (0.14), residues: 3523 helix: 0.15 (0.17), residues: 991 sheet: -0.92 (0.20), residues: 650 loop : -2.04 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 161 TYR 0.030 0.002 TYR D 279 PHE 0.035 0.002 PHE B 906 TRP 0.024 0.002 TRP D 168 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.01172 (29635) covalent geometry : angle 0.70823 (40305) SS BOND : bond 0.00425 ( 41) SS BOND : angle 2.00192 ( 82) hydrogen bonds : bond 0.04510 ( 1037) hydrogen bonds : angle 5.86452 ( 2913) Misc. bond : bond 0.00047 ( 1) link_BETA1-4 : bond 0.00563 ( 16) link_BETA1-4 : angle 2.17052 ( 48) link_NAG-ASN : bond 0.00583 ( 43) link_NAG-ASN : angle 3.17231 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8646 (t70) cc_final: 0.8177 (t0) REVERT: A 869 MET cc_start: 0.9185 (ptp) cc_final: 0.8927 (ptp) REVERT: B 697 MET cc_start: 0.8534 (ttm) cc_final: 0.8225 (ttt) REVERT: C 515 PHE cc_start: 0.7544 (m-80) cc_final: 0.6984 (m-80) REVERT: C 900 MET cc_start: 0.9199 (mmp) cc_final: 0.8776 (mmt) REVERT: C 1029 MET cc_start: 0.8907 (tpp) cc_final: 0.8333 (tmm) REVERT: D 62 MET cc_start: 0.9090 (ptp) cc_final: 0.8884 (ptp) REVERT: D 270 MET cc_start: 0.7609 (tmm) cc_final: 0.5229 (ptm) REVERT: D 323 MET cc_start: 0.6418 (tpt) cc_final: 0.6164 (tpp) REVERT: D 360 MET cc_start: 0.7133 (mmm) cc_final: 0.6569 (mmt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1602 time to fit residues: 26.7637 Evaluate side-chains 77 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 260 optimal weight: 2.9990 chunk 132 optimal weight: 0.0970 chunk 75 optimal weight: 0.2980 chunk 314 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 332 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 340 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 417 HIS ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** 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 = 0.3783 r_free = 0.3783 target = 0.082240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057257 restraints weight = 158931.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057144 restraints weight = 103013.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057043 restraints weight = 82217.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057222 restraints weight = 75865.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.057531 restraints weight = 66164.921| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.334 29736 Z= 0.443 Angle : 0.688 17.263 40564 Z= 0.348 Chirality : 0.047 0.479 4705 Planarity : 0.004 0.069 5132 Dihedral : 7.374 101.960 5064 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.63 (0.14), residues: 3523 helix: 0.38 (0.17), residues: 980 sheet: -0.91 (0.19), residues: 653 loop : -2.00 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 161 TYR 0.030 0.001 TYR D 279 PHE 0.024 0.001 PHE B 906 TRP 0.021 0.001 TRP D 168 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.01128 (29635) covalent geometry : angle 0.65905 (40305) SS BOND : bond 0.00411 ( 41) SS BOND : angle 1.79124 ( 82) hydrogen bonds : bond 0.04204 ( 1037) hydrogen bonds : angle 5.70171 ( 2913) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00501 ( 16) link_BETA1-4 : angle 2.10693 ( 48) link_NAG-ASN : bond 0.00522 ( 43) link_NAG-ASN : angle 3.05143 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4448.85 seconds wall clock time: 77 minutes 59.86 seconds (4679.86 seconds total)