Starting phenix.real_space_refine on Sun Jul 5 09:00:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z85_14543/07_2026/7z85_14543.cif" } resolution = 3.1 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= 0.005 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 123 5.16 5 C 17084 2.51 5 N 4396 2.21 5 O 5231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26834 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} bond proxies already assigned to first conformer: 985 Chain: "D" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} bond proxies already assigned to first conformer: 985 Chain: "E" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} bond proxies already assigned to first conformer: 985 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 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 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 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 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.17, per 1000 atoms: 0.23 Number of scatterers: 26834 At special positions: 0 Unit cell: (127.2, 136.74, 215.18, 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 123 16.00 O 5231 8.00 N 4396 7.00 C 17084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.03 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=2.03 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=2.04 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 ACYS F 22 " - pdb=" SG ACYS F 96 " distance=2.04 Simple disulfide: pdb=" SG BCYS F 22 " - pdb=" SG BCYS F 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS D 22 " - pdb=" SG ACYS D 96 " distance=2.03 Simple disulfide: pdb=" SG BCYS D 22 " - pdb=" SG BCYS D 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS E 22 " - pdb=" SG ACYS E 96 " distance=2.03 Simple disulfide: pdb=" SG BCYS E 22 " - pdb=" SG BCYS E 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 53 sheets defined 25.0% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.801A 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 384 through 389 removed outlier: 3.501A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.357A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.879A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.693A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.730A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.317A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.943A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.787A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.666A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.409A 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 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.726A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.681A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.249A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.951A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.632A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.334A 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 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.721A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.591A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.744A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.261A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.026A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.809A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.146A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.726A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.565A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.795A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.949A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.871A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.805A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.702A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.332A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.851A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.207A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.811A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.660A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.807A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.811A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.303A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.690A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.403A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.636A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.967A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.508A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.787A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.148A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.533A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.694A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.836A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.800A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.215A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.447A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.714A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.872A pdb=" N ALA F 33 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.856A pdb=" N TYR F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.556A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.542A pdb=" N ALA D 33 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.738A pdb=" N VAL E 5 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.380A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA E 33 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.380A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3153 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: 6.05 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8453 1.34 - 1.46: 6979 1.46 - 1.59: 11837 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 27425 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG C1408 " pdb=" O5 NAG C1408 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.355 0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" C1 NAG P 1 " pdb=" C2 NAG P 1 " ideal model delta sigma weight residual 1.532 1.481 0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 36427 2.49 - 4.98: 838 4.98 - 7.47: 46 7.47 - 9.96: 7 9.96 - 12.45: 1 Bond angle restraints: 37319 Sorted by residual: angle pdb=" C SER F 25 " pdb=" N GLY F 26 " pdb=" CA GLY F 26 " ideal model delta sigma weight residual 121.86 128.50 -6.64 8.50e-01 1.38e+00 6.11e+01 angle pdb=" C SER D 25 " pdb=" N GLY D 26 " pdb=" CA GLY D 26 " ideal model delta sigma weight residual 121.86 125.64 -3.78 8.50e-01 1.38e+00 1.98e+01 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 120.19 -6.29 1.80e+00 3.09e-01 1.22e+01 angle pdb=" N SER F 25 " pdb=" CA SER F 25 " pdb=" C SER F 25 " ideal model delta sigma weight residual 109.41 114.70 -5.29 1.52e+00 4.33e-01 1.21e+01 ... (remaining 37314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 14499 17.24 - 34.48: 979 34.48 - 51.72: 213 51.72 - 68.96: 36 68.96 - 86.19: 29 Dihedral angle restraints: 15756 sinusoidal: 6023 harmonic: 9733 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.20 -82.20 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -160.82 74.82 1 1.00e+01 1.00e-02 7.09e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3583 0.067 - 0.134: 774 0.134 - 0.202: 62 0.202 - 0.269: 10 0.269 - 0.336: 2 Chirality restraints: 4431 Sorted by residual: chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4428 not shown) Planarity restraints: 4765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ALA C 958 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA C 958 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU C 959 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C ALA A 958 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 958 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 959 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 958 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ALA B 958 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA B 958 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 959 " 0.020 2.00e-02 2.50e+03 ... (remaining 4762 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1047 2.70 - 3.25: 25917 3.25 - 3.80: 43069 3.80 - 4.35: 55729 4.35 - 4.90: 94298 Nonbonded interactions: 220060 Sorted by model distance: nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.156 3.040 nonbonded pdb=" NH2 ARG B 328 " pdb=" OE1 GLN B 580 " model vdw 2.183 3.120 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.206 3.040 nonbonded pdb=" ND2 ASN C 437 " pdb=" OE1 GLN C 506 " model vdw 2.209 3.120 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.213 3.120 ... (remaining 220055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 through 1408 \ )) } ncs_group { reference = (chain 'D' and (resid 2 through 21 or resid 23 through 95 or resid 97 through 12 \ 6)) selection = (chain 'E' and (resid 2 through 21 or resid 23 through 95 or resid 97 through 12 \ 6)) selection = (chain 'F' and (resid 2 through 21 or resid 23 through 95 or resid 97 through 12 \ 6)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.170 Find NCS groups from input model: 1.000 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 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 : 0.007 0.079 27536 Z= 0.311 Angle : 0.904 12.451 37607 Z= 0.493 Chirality : 0.054 0.336 4431 Planarity : 0.004 0.056 4719 Dihedral : 12.823 86.194 9373 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 0.99 % Allowed : 4.66 % Favored : 94.35 % 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: -0.88 (0.13), residues: 3290 helix: -0.39 (0.19), residues: 661 sheet: 0.05 (0.17), residues: 801 loop : -0.92 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG B 577 TYR 0.023 0.003 TYR B 495 PHE 0.033 0.003 PHE E 37 TRP 0.032 0.002 TRP F 36 HIS 0.013 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.31 (27425) covalent geometry : angle 0.88299 / 0.49 (37319) SS BOND : bond 0.00508 / 0.31 ( 45) SS BOND : angle 1.43301 / 0.92 ( 90) hydrogen bonds : bond 0.15822 / 10.19 ( 1163) hydrogen bonds : angle 7.19430 / 4.95 ( 3153) link_BETA1-4 : bond 0.00817 / 0.47 ( 20) link_BETA1-4 : angle 1.74373 / 1.17 ( 60) link_NAG-ASN : bond 0.00486 / 0.32 ( 46) link_NAG-ASN : angle 3.03043 / 2.02 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 451 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6959 (m-80) cc_final: 0.6594 (m-80) REVERT: A 45 SER cc_start: 0.7951 (p) cc_final: 0.7689 (m) REVERT: A 120 VAL cc_start: 0.6438 (t) cc_final: 0.5971 (p) REVERT: A 129 LYS cc_start: 0.6586 (pttt) cc_final: 0.6373 (ptpt) REVERT: A 165 ASN cc_start: 0.5758 (m-40) cc_final: 0.4127 (t0) REVERT: A 230 PRO cc_start: 0.6957 (Cg_endo) cc_final: 0.6398 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.6666 (ttm170) REVERT: A 309 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6978 (mm-30) REVERT: A 319 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7146 (ttm-80) REVERT: A 519 HIS cc_start: 0.4690 (OUTLIER) cc_final: 0.4366 (t70) REVERT: A 702 GLU cc_start: 0.7865 (pt0) cc_final: 0.7567 (tt0) REVERT: A 762 GLN cc_start: 0.7722 (tt0) cc_final: 0.7504 (mt0) REVERT: A 773 GLU cc_start: 0.6793 (tt0) cc_final: 0.6561 (tt0) REVERT: A 796 ASP cc_start: 0.6864 (t0) cc_final: 0.5814 (p0) REVERT: A 817 PHE cc_start: 0.7334 (t80) cc_final: 0.7022 (t80) REVERT: A 855 PHE cc_start: 0.7182 (m-80) cc_final: 0.6945 (m-80) REVERT: A 868 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7048 (mp0) REVERT: A 950 ASP cc_start: 0.7648 (t70) cc_final: 0.7185 (m-30) REVERT: A 1045 LYS cc_start: 0.7560 (mtpp) cc_final: 0.7346 (tttm) REVERT: A 1135 ASN cc_start: 0.8532 (t0) cc_final: 0.8318 (t0) REVERT: B 102 ARG cc_start: 0.6123 (mtt180) cc_final: 0.5809 (mmm160) REVERT: B 205 SER cc_start: 0.8441 (p) cc_final: 0.8149 (p) REVERT: B 269 TYR cc_start: 0.7343 (m-80) cc_final: 0.6998 (m-10) REVERT: B 271 GLN cc_start: 0.6757 (mt0) cc_final: 0.6292 (mm-40) REVERT: B 303 LEU cc_start: 0.6587 (mt) cc_final: 0.6235 (mp) REVERT: B 305 SER cc_start: 0.8584 (t) cc_final: 0.8361 (p) REVERT: B 316 SER cc_start: 0.7778 (t) cc_final: 0.7528 (p) REVERT: B 342 PHE cc_start: 0.7569 (m-80) cc_final: 0.7298 (m-80) REVERT: B 353 TRP cc_start: 0.7363 (p-90) cc_final: 0.6876 (p-90) REVERT: B 365 TYR cc_start: 0.6204 (m-80) cc_final: 0.5963 (m-80) REVERT: B 389 ASP cc_start: 0.7416 (m-30) cc_final: 0.6871 (t70) REVERT: B 453 TYR cc_start: 0.6790 (p90) cc_final: 0.6486 (p90) REVERT: B 508 TYR cc_start: 0.6223 (m-80) cc_final: 0.5678 (m-80) REVERT: B 592 PHE cc_start: 0.6697 (p90) cc_final: 0.6406 (p90) REVERT: B 646 ARG cc_start: 0.7509 (tpp80) cc_final: 0.6949 (mtp180) REVERT: B 658 ASN cc_start: 0.6819 (m-40) cc_final: 0.6453 (t0) REVERT: B 702 GLU cc_start: 0.8192 (tt0) cc_final: 0.7512 (mm-30) REVERT: B 773 GLU cc_start: 0.7030 (tt0) cc_final: 0.6725 (tt0) REVERT: B 790 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7405 (mmmt) REVERT: B 804 GLN cc_start: 0.8741 (mt0) cc_final: 0.8274 (mm110) REVERT: B 868 GLU cc_start: 0.7113 (pt0) cc_final: 0.6630 (mp0) REVERT: B 935 GLN cc_start: 0.6806 (mt0) cc_final: 0.6468 (mt0) REVERT: B 1010 GLN cc_start: 0.8127 (mm110) cc_final: 0.7907 (mm-40) REVERT: B 1038 LYS cc_start: 0.8291 (mttm) cc_final: 0.7940 (mmmt) REVERT: B 1045 LYS cc_start: 0.8359 (tttp) cc_final: 0.7765 (mptt) REVERT: B 1142 GLN cc_start: 0.6515 (mm-40) cc_final: 0.6295 (tt0) REVERT: C 45 SER cc_start: 0.7994 (p) cc_final: 0.7371 (t) REVERT: C 52 GLN cc_start: 0.7721 (tt0) cc_final: 0.7095 (tt0) REVERT: C 140 PHE cc_start: 0.5376 (p90) cc_final: 0.5084 (p90) REVERT: C 237 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7128 (mtm110) REVERT: C 307 THR cc_start: 0.7444 (p) cc_final: 0.7215 (p) REVERT: C 365 TYR cc_start: 0.6621 (m-80) cc_final: 0.6371 (m-80) REVERT: C 396 TYR cc_start: 0.6644 (m-80) cc_final: 0.6373 (m-10) REVERT: C 427 ASP cc_start: 0.7023 (m-30) cc_final: 0.6035 (t70) REVERT: C 434 ILE cc_start: 0.6067 (mt) cc_final: 0.5745 (mm) REVERT: C 512 VAL cc_start: 0.8162 (t) cc_final: 0.7762 (p) REVERT: C 558 LYS cc_start: 0.7337 (mmtt) cc_final: 0.7121 (mttm) REVERT: C 577 ARG cc_start: 0.6885 (ttm-80) cc_final: 0.6672 (ttm-80) REVERT: C 606 ASN cc_start: 0.8424 (m-40) cc_final: 0.8147 (m-40) REVERT: C 646 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7397 (tpt90) REVERT: C 674 TYR cc_start: 0.8289 (t80) cc_final: 0.8040 (t80) REVERT: C 675 GLN cc_start: 0.7246 (mt0) cc_final: 0.6998 (mm-40) REVERT: C 755 GLN cc_start: 0.7642 (mt0) cc_final: 0.7141 (mm110) REVERT: C 758 SER cc_start: 0.6612 (m) cc_final: 0.6103 (p) REVERT: C 912 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 1005 GLN cc_start: 0.8072 (mt0) cc_final: 0.7767 (tp40) REVERT: C 1012 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 1038 LYS cc_start: 0.8010 (mttm) cc_final: 0.7541 (mmtp) REVERT: C 1050 MET cc_start: 0.8853 (ptt) cc_final: 0.8641 (ptm) REVERT: C 1144 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6680 (mm-30) REVERT: F 29 PHE cc_start: 0.1969 (OUTLIER) cc_final: 0.1537 (t80) REVERT: F 83 MET cc_start: 0.2958 (mtp) cc_final: 0.1513 (tmm) outliers start: 27 outliers final: 10 residues processed: 473 average time/residue: 0.1791 time to fit residues: 132.2059 Evaluate side-chains 291 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 277 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain E residue 29 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 613 GLN A 804 GLN A 935 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 437 ASN B1101 HIS C 30 ASN C 125 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 949 GLN C1010 GLN C1048 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.203844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161143 restraints weight = 62597.811| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.90 r_work: 0.3214 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27536 Z= 0.171 Angle : 0.641 11.998 37607 Z= 0.325 Chirality : 0.046 0.305 4431 Planarity : 0.004 0.136 4719 Dihedral : 5.234 47.665 3631 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.80 % Allowed : 7.27 % Favored : 90.93 % 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: 0.10 (0.14), residues: 3290 helix: 1.16 (0.20), residues: 656 sheet: 0.29 (0.16), residues: 838 loop : -0.41 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 45 TYR 0.031 0.001 TYR C 508 PHE 0.018 0.002 PHE C 592 TRP 0.011 0.001 TRP E 117 HIS 0.010 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (27425) covalent geometry : angle 0.61879 / 0.32 (37319) SS BOND : bond 0.00369 / 0.23 ( 45) SS BOND : angle 1.74458 / 0.98 ( 90) hydrogen bonds : bond 0.04526 / 2.93 ( 1163) hydrogen bonds : angle 6.00156 / 4.09 ( 3153) link_BETA1-4 : bond 0.00481 / 0.24 ( 20) link_BETA1-4 : angle 1.16226 / 0.76 ( 60) link_NAG-ASN : bond 0.00430 / 0.27 ( 46) link_NAG-ASN : angle 2.42632 / 1.53 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7332 (t) cc_final: 0.6912 (p) REVERT: A 129 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7176 (ptpp) REVERT: A 165 ASN cc_start: 0.5739 (m-40) cc_final: 0.5200 (t0) REVERT: A 309 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7852 (mm-30) REVERT: A 762 GLN cc_start: 0.8428 (tt0) cc_final: 0.8180 (mt0) REVERT: A 817 PHE cc_start: 0.8553 (t80) cc_final: 0.8232 (t80) REVERT: A 950 ASP cc_start: 0.8322 (t70) cc_final: 0.8098 (m-30) REVERT: B 28 TYR cc_start: 0.6857 (m-10) cc_final: 0.6617 (m-80) REVERT: B 271 GLN cc_start: 0.7854 (mt0) cc_final: 0.7308 (mm110) REVERT: B 316 SER cc_start: 0.8557 (t) cc_final: 0.8353 (p) REVERT: B 389 ASP cc_start: 0.7564 (m-30) cc_final: 0.7106 (t70) REVERT: B 396 TYR cc_start: 0.7731 (m-80) cc_final: 0.7524 (m-80) REVERT: B 507 PRO cc_start: 0.6103 (Cg_exo) cc_final: 0.5768 (Cg_endo) REVERT: B 508 TYR cc_start: 0.5913 (m-80) cc_final: 0.5255 (m-80) REVERT: B 1141 LEU cc_start: 0.7499 (tp) cc_final: 0.7291 (tp) REVERT: C 45 SER cc_start: 0.8437 (p) cc_final: 0.8168 (t) REVERT: C 65 PHE cc_start: 0.7047 (m-80) cc_final: 0.6490 (m-80) REVERT: C 140 PHE cc_start: 0.5708 (p90) cc_final: 0.5388 (p90) REVERT: C 237 ARG cc_start: 0.8006 (mtt180) cc_final: 0.7490 (mtm110) REVERT: C 427 ASP cc_start: 0.6188 (m-30) cc_final: 0.5490 (t70) REVERT: C 433 VAL cc_start: 0.8410 (t) cc_final: 0.8155 (p) REVERT: C 755 GLN cc_start: 0.8346 (mt0) cc_final: 0.8030 (mm110) REVERT: C 1081 ILE cc_start: 0.8045 (pt) cc_final: 0.7756 (pt) REVERT: F 29 PHE cc_start: 0.2384 (OUTLIER) cc_final: 0.2097 (t80) REVERT: F 83 MET cc_start: 0.2405 (mtp) cc_final: 0.0393 (tmm) REVERT: E 12 MET cc_start: 0.2747 (ppp) cc_final: 0.2338 (ppp) REVERT: E 34 MET cc_start: 0.4545 (mtm) cc_final: 0.4061 (mtm) outliers start: 50 outliers final: 30 residues processed: 345 average time/residue: 0.1684 time to fit residues: 92.5329 Evaluate side-chains 274 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain D residue 27 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 140 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 222 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.203979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.160693 restraints weight = 54035.651| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.82 r_work: 0.3127 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 27536 Z= 0.159 Angle : 0.602 13.447 37607 Z= 0.304 Chirality : 0.045 0.327 4431 Planarity : 0.004 0.079 4719 Dihedral : 4.902 49.718 3618 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.19 % Allowed : 8.12 % Favored : 89.70 % 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: 0.31 (0.14), residues: 3290 helix: 1.76 (0.21), residues: 639 sheet: 0.27 (0.16), residues: 856 loop : -0.35 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 45 TYR 0.019 0.001 TYR A 369 PHE 0.016 0.002 PHE B 565 TRP 0.015 0.001 TRP D 53 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (27425) covalent geometry : angle 0.57817 / 0.30 (37319) SS BOND : bond 0.00628 / 0.34 ( 45) SS BOND : angle 1.71780 / 1.04 ( 90) hydrogen bonds : bond 0.04324 / 2.79 ( 1163) hydrogen bonds : angle 5.76592 / 3.90 ( 3153) link_BETA1-4 : bond 0.00354 / 0.19 ( 20) link_BETA1-4 : angle 1.19408 / 0.79 ( 60) link_NAG-ASN : bond 0.00273 / 0.18 ( 46) link_NAG-ASN : angle 2.41910 / 1.60 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7463 (t) cc_final: 0.6982 (p) REVERT: A 129 LYS cc_start: 0.7446 (pttt) cc_final: 0.6934 (ptpp) REVERT: A 165 ASN cc_start: 0.5621 (m-40) cc_final: 0.4774 (t0) REVERT: A 309 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7714 (mm-30) REVERT: A 817 PHE cc_start: 0.8513 (t80) cc_final: 0.8158 (t80) REVERT: B 102 ARG cc_start: 0.6787 (mtp180) cc_final: 0.6521 (mmm-85) REVERT: B 269 TYR cc_start: 0.7443 (m-10) cc_final: 0.7196 (m-80) REVERT: B 271 GLN cc_start: 0.7624 (mt0) cc_final: 0.6918 (mm110) REVERT: B 316 SER cc_start: 0.8673 (t) cc_final: 0.8418 (p) REVERT: B 389 ASP cc_start: 0.7599 (m-30) cc_final: 0.6898 (t70) REVERT: B 417 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7279 (mtpt) REVERT: B 427 ASP cc_start: 0.6537 (m-30) cc_final: 0.6222 (m-30) REVERT: B 507 PRO cc_start: 0.6269 (Cg_exo) cc_final: 0.5936 (Cg_endo) REVERT: B 508 TYR cc_start: 0.5921 (m-80) cc_final: 0.5040 (m-80) REVERT: B 1141 LEU cc_start: 0.7463 (tp) cc_final: 0.7246 (tp) REVERT: C 45 SER cc_start: 0.8371 (p) cc_final: 0.8119 (t) REVERT: C 65 PHE cc_start: 0.7146 (m-80) cc_final: 0.6605 (m-80) REVERT: C 140 PHE cc_start: 0.5996 (p90) cc_final: 0.5456 (p90) REVERT: C 237 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7159 (mtm110) REVERT: C 427 ASP cc_start: 0.6430 (m-30) cc_final: 0.5448 (t70) REVERT: C 508 TYR cc_start: 0.7220 (m-80) cc_final: 0.6528 (m-80) REVERT: C 675 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7128 (mm-40) REVERT: C 755 GLN cc_start: 0.8345 (mt0) cc_final: 0.7933 (mm110) REVERT: C 1081 ILE cc_start: 0.8027 (pt) cc_final: 0.7742 (pt) REVERT: F 34 MET cc_start: 0.3164 (mpp) cc_final: 0.2255 (mpp) REVERT: F 83 MET cc_start: 0.1914 (mtp) cc_final: 0.0204 (tmm) REVERT: E 34 MET cc_start: 0.4516 (mtm) cc_final: 0.3979 (mtm) outliers start: 61 outliers final: 43 residues processed: 313 average time/residue: 0.1699 time to fit residues: 86.2130 Evaluate side-chains 280 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain D residue 27 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 48 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 239 GLN A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.202707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159843 restraints weight = 58040.416| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.73 r_work: 0.3098 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27536 Z= 0.191 Angle : 0.614 11.273 37607 Z= 0.310 Chirality : 0.046 0.464 4431 Planarity : 0.004 0.058 4719 Dihedral : 4.950 59.278 3616 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.89 % Allowed : 8.47 % Favored : 88.64 % 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: 0.26 (0.14), residues: 3290 helix: 1.77 (0.21), residues: 639 sheet: 0.23 (0.16), residues: 852 loop : -0.40 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.019 0.001 TYR A 369 PHE 0.017 0.002 PHE C 400 TRP 0.011 0.001 TRP B 436 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (27425) covalent geometry : angle 0.58865 / 0.30 (37319) SS BOND : bond 0.00581 / 0.34 ( 45) SS BOND : angle 1.98677 / 1.21 ( 90) hydrogen bonds : bond 0.04355 / 2.82 ( 1163) hydrogen bonds : angle 5.72809 / 3.86 ( 3153) link_BETA1-4 : bond 0.00327 / 0.17 ( 20) link_BETA1-4 : angle 1.18672 / 0.78 ( 60) link_NAG-ASN : bond 0.00405 / 0.25 ( 46) link_NAG-ASN : angle 2.40493 / 1.50 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 254 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7421 (t) cc_final: 0.6969 (p) REVERT: A 129 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6911 (ptpp) REVERT: A 165 ASN cc_start: 0.5457 (m-40) cc_final: 0.4713 (t0) REVERT: A 309 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7814 (mm-30) REVERT: A 734 THR cc_start: 0.8868 (m) cc_final: 0.8636 (p) REVERT: A 817 PHE cc_start: 0.8662 (t80) cc_final: 0.8290 (t80) REVERT: B 102 ARG cc_start: 0.6772 (mtp180) cc_final: 0.6514 (mmm-85) REVERT: B 269 TYR cc_start: 0.7641 (m-10) cc_final: 0.7369 (m-80) REVERT: B 271 GLN cc_start: 0.7532 (mt0) cc_final: 0.6904 (mm110) REVERT: B 360 ASN cc_start: 0.7299 (m-40) cc_final: 0.6980 (m-40) REVERT: B 417 LYS cc_start: 0.7567 (ttmm) cc_final: 0.7258 (mtpt) REVERT: B 427 ASP cc_start: 0.6591 (m-30) cc_final: 0.6291 (m-30) REVERT: B 507 PRO cc_start: 0.6212 (Cg_exo) cc_final: 0.5851 (Cg_endo) REVERT: B 508 TYR cc_start: 0.5902 (m-80) cc_final: 0.5156 (m-80) REVERT: B 529 LYS cc_start: 0.7348 (mttm) cc_final: 0.6845 (mtmm) REVERT: C 45 SER cc_start: 0.8417 (p) cc_final: 0.8145 (t) REVERT: C 65 PHE cc_start: 0.7105 (m-80) cc_final: 0.6498 (m-80) REVERT: C 140 PHE cc_start: 0.6089 (p90) cc_final: 0.5501 (p90) REVERT: C 237 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7080 (mtm110) REVERT: C 427 ASP cc_start: 0.6409 (m-30) cc_final: 0.5481 (t70) REVERT: C 508 TYR cc_start: 0.7459 (m-80) cc_final: 0.6894 (m-80) REVERT: C 755 GLN cc_start: 0.8370 (mt0) cc_final: 0.7945 (mm110) REVERT: C 1081 ILE cc_start: 0.8049 (pt) cc_final: 0.7776 (pt) REVERT: F 29 PHE cc_start: 0.1650 (OUTLIER) cc_final: 0.1279 (t80) REVERT: E 34 MET cc_start: 0.4708 (mtm) cc_final: 0.4034 (mtm) outliers start: 80 outliers final: 55 residues processed: 312 average time/residue: 0.1723 time to fit residues: 86.9470 Evaluate side-chains 300 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain D residue 27 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 146 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 306 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.203218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160533 restraints weight = 61659.243| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.84 r_work: 0.3091 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27536 Z= 0.155 Angle : 0.578 12.520 37607 Z= 0.291 Chirality : 0.044 0.446 4431 Planarity : 0.004 0.052 4719 Dihedral : 4.793 48.825 3616 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.72 % Allowed : 9.17 % Favored : 88.11 % 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: 0.31 (0.14), residues: 3290 helix: 1.90 (0.21), residues: 639 sheet: 0.22 (0.16), residues: 855 loop : -0.38 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.018 0.001 TYR A 369 PHE 0.021 0.001 PHE A 32 TRP 0.011 0.001 TRP B 436 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (27425) covalent geometry : angle 0.55201 / 0.28 (37319) SS BOND : bond 0.00418 / 0.24 ( 45) SS BOND : angle 1.91556 / 1.10 ( 90) hydrogen bonds : bond 0.04076 / 2.63 ( 1163) hydrogen bonds : angle 5.60403 / 3.77 ( 3153) link_BETA1-4 : bond 0.00325 / 0.17 ( 20) link_BETA1-4 : angle 1.11637 / 0.74 ( 60) link_NAG-ASN : bond 0.00229 / 0.15 ( 46) link_NAG-ASN : angle 2.36075 / 1.50 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7612 (m-10) cc_final: 0.7341 (m-10) REVERT: A 120 VAL cc_start: 0.7396 (t) cc_final: 0.6871 (p) REVERT: A 129 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6861 (ptpp) REVERT: A 165 ASN cc_start: 0.5434 (m-40) cc_final: 0.4663 (t0) REVERT: A 309 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7848 (mm-30) REVERT: A 734 THR cc_start: 0.8863 (m) cc_final: 0.8642 (p) REVERT: A 817 PHE cc_start: 0.8670 (t80) cc_final: 0.8285 (t80) REVERT: B 102 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6517 (mmm-85) REVERT: B 269 TYR cc_start: 0.7625 (m-10) cc_final: 0.7370 (m-80) REVERT: B 271 GLN cc_start: 0.7558 (mt0) cc_final: 0.6917 (mm110) REVERT: B 329 PHE cc_start: 0.7353 (m-80) cc_final: 0.6991 (m-80) REVERT: B 360 ASN cc_start: 0.7313 (m-40) cc_final: 0.7031 (m-40) REVERT: B 389 ASP cc_start: 0.7818 (m-30) cc_final: 0.7121 (t70) REVERT: B 417 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7253 (mtpt) REVERT: B 427 ASP cc_start: 0.6610 (m-30) cc_final: 0.6319 (m-30) REVERT: B 507 PRO cc_start: 0.6195 (Cg_exo) cc_final: 0.5834 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6083 (m-80) cc_final: 0.5325 (m-80) REVERT: B 529 LYS cc_start: 0.7487 (mttm) cc_final: 0.6942 (mtmm) REVERT: B 544 ASN cc_start: 0.8013 (m-40) cc_final: 0.7772 (m110) REVERT: C 45 SER cc_start: 0.8403 (p) cc_final: 0.8142 (t) REVERT: C 65 PHE cc_start: 0.7125 (m-80) cc_final: 0.6495 (m-80) REVERT: C 140 PHE cc_start: 0.6134 (p90) cc_final: 0.5510 (p90) REVERT: C 237 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7090 (mtm110) REVERT: C 427 ASP cc_start: 0.6400 (m-30) cc_final: 0.5571 (t70) REVERT: C 508 TYR cc_start: 0.7203 (m-80) cc_final: 0.6469 (m-80) REVERT: C 755 GLN cc_start: 0.8414 (mt0) cc_final: 0.7972 (mm110) REVERT: C 1081 ILE cc_start: 0.8042 (pt) cc_final: 0.7766 (pt) REVERT: E 34 MET cc_start: 0.4767 (mtm) cc_final: 0.4038 (mtm) outliers start: 75 outliers final: 58 residues processed: 299 average time/residue: 0.1731 time to fit residues: 84.0098 Evaluate side-chains 291 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain D residue 27 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 306 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 354 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 935 GLN B1106 GLN B1119 ASN C 239 GLN C 450 ASN C 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.200095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157837 restraints weight = 63224.009| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.89 r_work: 0.3154 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 27536 Z= 0.293 Angle : 0.735 26.560 37607 Z= 0.359 Chirality : 0.050 0.747 4431 Planarity : 0.005 0.051 4719 Dihedral : 5.240 54.248 3616 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.11 % Allowed : 9.42 % Favored : 87.47 % 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: -0.01 (0.14), residues: 3290 helix: 1.48 (0.21), residues: 635 sheet: 0.05 (0.16), residues: 847 loop : -0.54 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 319 TYR 0.021 0.002 TYR B 200 PHE 0.021 0.002 PHE C1121 TRP 0.016 0.002 TRP E 36 HIS 0.008 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.29 (27425) covalent geometry : angle 0.68316 / 0.35 (37319) SS BOND : bond 0.00629 / 0.36 ( 45) SS BOND : angle 2.47251 / 1.43 ( 90) hydrogen bonds : bond 0.04881 / 3.16 ( 1163) hydrogen bonds : angle 5.83009 / 3.92 ( 3153) link_BETA1-4 : bond 0.00492 / 0.20 ( 20) link_BETA1-4 : angle 1.46185 / 0.98 ( 60) link_NAG-ASN : bond 0.00353 / 0.23 ( 46) link_NAG-ASN : angle 3.99867 / 3.06 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 235 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7437 (t) cc_final: 0.6982 (p) REVERT: A 129 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7126 (ptpp) REVERT: A 165 ASN cc_start: 0.5333 (m-40) cc_final: 0.4864 (t0) REVERT: A 734 THR cc_start: 0.8878 (m) cc_final: 0.8653 (p) REVERT: A 776 LYS cc_start: 0.8859 (tttt) cc_final: 0.8599 (ttpp) REVERT: B 271 GLN cc_start: 0.7597 (mt0) cc_final: 0.7041 (mm110) REVERT: B 417 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7353 (mtpt) REVERT: B 427 ASP cc_start: 0.6631 (m-30) cc_final: 0.6356 (m-30) REVERT: B 507 PRO cc_start: 0.5957 (Cg_exo) cc_final: 0.5705 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6194 (m-80) cc_final: 0.5620 (m-80) REVERT: B 529 LYS cc_start: 0.7542 (mttm) cc_final: 0.7339 (mtmm) REVERT: C 65 PHE cc_start: 0.7106 (m-80) cc_final: 0.6486 (m-80) REVERT: C 140 PHE cc_start: 0.6047 (p90) cc_final: 0.5510 (p90) REVERT: C 237 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7285 (mtm110) REVERT: C 357 ARG cc_start: 0.7361 (ttp80) cc_final: 0.6994 (tpt-90) REVERT: C 508 TYR cc_start: 0.7082 (m-80) cc_final: 0.6816 (m-80) REVERT: C 569 ILE cc_start: 0.7260 (tp) cc_final: 0.6654 (mm) REVERT: C 755 GLN cc_start: 0.8459 (mt0) cc_final: 0.8060 (mm110) REVERT: C 1144 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: E 34 MET cc_start: 0.5045 (mtm) cc_final: 0.4193 (mtm) outliers start: 87 outliers final: 66 residues processed: 301 average time/residue: 0.1750 time to fit residues: 85.6858 Evaluate side-chains 287 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 219 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain F residue 30 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 88 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.202900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.162259 restraints weight = 71117.262| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.98 r_work: 0.3354 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27536 Z= 0.134 Angle : 0.598 22.785 37607 Z= 0.294 Chirality : 0.045 0.504 4431 Planarity : 0.004 0.045 4719 Dihedral : 4.818 52.828 3612 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.08 % Allowed : 10.44 % Favored : 87.47 % 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: 0.19 (0.14), residues: 3290 helix: 1.82 (0.21), residues: 638 sheet: 0.14 (0.17), residues: 856 loop : -0.47 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 319 TYR 0.019 0.001 TYR E 95 PHE 0.018 0.001 PHE A 32 TRP 0.012 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (27425) covalent geometry : angle 0.54879 / 0.28 (37319) SS BOND : bond 0.00363 / 0.22 ( 45) SS BOND : angle 2.05152 / 1.19 ( 90) hydrogen bonds : bond 0.03977 / 2.56 ( 1163) hydrogen bonds : angle 5.58986 / 3.76 ( 3153) link_BETA1-4 : bond 0.00365 / 0.19 ( 20) link_BETA1-4 : angle 1.04302 / 0.70 ( 60) link_NAG-ASN : bond 0.00361 / 0.24 ( 46) link_NAG-ASN : angle 3.57622 / 2.71 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7174 (t) cc_final: 0.6814 (p) REVERT: A 129 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7203 (ptpp) REVERT: A 165 ASN cc_start: 0.4999 (m-40) cc_final: 0.4756 (t0) REVERT: A 567 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8207 (mtt180) REVERT: A 734 THR cc_start: 0.8779 (m) cc_final: 0.8527 (p) REVERT: A 817 PHE cc_start: 0.8710 (t80) cc_final: 0.8405 (t80) REVERT: B 237 ARG cc_start: 0.6936 (ttp-170) cc_final: 0.6550 (ttm170) REVERT: B 269 TYR cc_start: 0.7382 (m-10) cc_final: 0.7150 (m-80) REVERT: B 271 GLN cc_start: 0.7673 (mt0) cc_final: 0.7240 (mm110) REVERT: B 389 ASP cc_start: 0.7795 (m-30) cc_final: 0.7267 (t70) REVERT: B 417 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7453 (mtpt) REVERT: B 427 ASP cc_start: 0.6313 (m-30) cc_final: 0.6028 (m-30) REVERT: B 508 TYR cc_start: 0.5968 (m-80) cc_final: 0.5722 (m-80) REVERT: B 544 ASN cc_start: 0.8284 (m-40) cc_final: 0.8041 (m110) REVERT: C 140 PHE cc_start: 0.5995 (p90) cc_final: 0.5649 (p90) REVERT: C 237 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7515 (mtm110) REVERT: C 357 ARG cc_start: 0.7315 (ttp80) cc_final: 0.7094 (tpt-90) REVERT: C 427 ASP cc_start: 0.6128 (m-30) cc_final: 0.5739 (t70) REVERT: C 569 ILE cc_start: 0.7093 (tp) cc_final: 0.6471 (mm) REVERT: C 755 GLN cc_start: 0.8427 (mt0) cc_final: 0.8127 (mm110) REVERT: C 1081 ILE cc_start: 0.8001 (pt) cc_final: 0.7721 (pt) REVERT: C 1144 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: E 34 MET cc_start: 0.5017 (mtm) cc_final: 0.4311 (mtm) outliers start: 58 outliers final: 48 residues processed: 298 average time/residue: 0.1725 time to fit residues: 84.2613 Evaluate side-chains 283 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 276 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 322 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 HIS ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 935 GLN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.200963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.157631 restraints weight = 69008.041| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.03 r_work: 0.3104 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 27536 Z= 0.192 Angle : 0.641 22.439 37607 Z= 0.315 Chirality : 0.048 0.888 4431 Planarity : 0.004 0.045 4719 Dihedral : 4.951 53.470 3612 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.36 % Allowed : 10.66 % Favored : 86.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3290 helix: 1.75 (0.21), residues: 639 sheet: 0.09 (0.17), residues: 846 loop : -0.49 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.020 0.001 TYR E 95 PHE 0.025 0.002 PHE A 592 TRP 0.012 0.001 TRP B 436 HIS 0.007 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (27425) covalent geometry : angle 0.59894 / 0.30 (37319) SS BOND : bond 0.00449 / 0.28 ( 45) SS BOND : angle 2.15900 / 1.29 ( 90) hydrogen bonds : bond 0.04274 / 2.77 ( 1163) hydrogen bonds : angle 5.61275 / 3.77 ( 3153) link_BETA1-4 : bond 0.00465 / 0.19 ( 20) link_BETA1-4 : angle 1.18110 / 0.80 ( 60) link_NAG-ASN : bond 0.00447 / 0.31 ( 46) link_NAG-ASN : angle 3.35906 / 2.54 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5937 (mmt90) cc_final: 0.5383 (mtt-85) REVERT: A 120 VAL cc_start: 0.7457 (t) cc_final: 0.6998 (p) REVERT: A 129 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6936 (ptpp) REVERT: A 165 ASN cc_start: 0.5168 (m-40) cc_final: 0.4570 (t0) REVERT: A 230 PRO cc_start: 0.7397 (Cg_endo) cc_final: 0.6948 (Cg_exo) REVERT: A 734 THR cc_start: 0.8995 (m) cc_final: 0.8636 (p) REVERT: A 817 PHE cc_start: 0.8767 (t80) cc_final: 0.8371 (t80) REVERT: B 237 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6406 (ttm170) REVERT: B 271 GLN cc_start: 0.7628 (mt0) cc_final: 0.6963 (mm110) REVERT: B 389 ASP cc_start: 0.7835 (m-30) cc_final: 0.7117 (t70) REVERT: B 417 LYS cc_start: 0.7589 (ttmm) cc_final: 0.7207 (mtpt) REVERT: B 427 ASP cc_start: 0.6711 (m-30) cc_final: 0.6422 (m-30) REVERT: B 508 TYR cc_start: 0.6394 (m-80) cc_final: 0.5691 (m-80) REVERT: C 140 PHE cc_start: 0.6115 (p90) cc_final: 0.5496 (p90) REVERT: C 237 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7059 (mtm110) REVERT: C 357 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6815 (tpt-90) REVERT: C 427 ASP cc_start: 0.6495 (m-30) cc_final: 0.5610 (t70) REVERT: C 569 ILE cc_start: 0.7193 (tp) cc_final: 0.6563 (mm) REVERT: C 755 GLN cc_start: 0.8453 (mt0) cc_final: 0.8015 (mm110) REVERT: C 1081 ILE cc_start: 0.8087 (pt) cc_final: 0.7810 (pt) REVERT: C 1144 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7216 (mm-30) REVERT: F 34 MET cc_start: 0.1478 (mpp) cc_final: -0.0017 (ttp) REVERT: E 34 MET cc_start: 0.4844 (mtm) cc_final: 0.4165 (mtm) outliers start: 65 outliers final: 56 residues processed: 293 average time/residue: 0.1726 time to fit residues: 82.5375 Evaluate side-chains 293 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 317 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 287 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 253 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 544 ASN B 658 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.202993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160460 restraints weight = 51145.385| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.70 r_work: 0.3225 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27536 Z= 0.114 Angle : 0.563 17.728 37607 Z= 0.278 Chirality : 0.044 0.527 4431 Planarity : 0.003 0.045 4719 Dihedral : 4.598 50.625 3612 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.94 % Allowed : 11.08 % Favored : 86.98 % 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: 0.26 (0.14), residues: 3290 helix: 1.96 (0.21), residues: 639 sheet: 0.13 (0.17), residues: 845 loop : -0.42 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.019 0.001 TYR E 95 PHE 0.020 0.001 PHE A 592 TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (27425) covalent geometry : angle 0.52611 / 0.27 (37319) SS BOND : bond 0.00353 / 0.23 ( 45) SS BOND : angle 1.58541 / 0.94 ( 90) hydrogen bonds : bond 0.03711 / 2.39 ( 1163) hydrogen bonds : angle 5.45373 / 3.67 ( 3153) link_BETA1-4 : bond 0.00461 / 0.22 ( 20) link_BETA1-4 : angle 1.01645 / 0.68 ( 60) link_NAG-ASN : bond 0.00379 / 0.26 ( 46) link_NAG-ASN : angle 3.04907 / 2.32 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5911 (mmt90) cc_final: 0.5645 (ttt90) REVERT: A 120 VAL cc_start: 0.7350 (t) cc_final: 0.6879 (p) REVERT: A 129 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6998 (ptpp) REVERT: A 165 ASN cc_start: 0.5187 (m-40) cc_final: 0.4714 (t0) REVERT: A 230 PRO cc_start: 0.7394 (Cg_endo) cc_final: 0.6976 (Cg_exo) REVERT: A 567 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8156 (mtt180) REVERT: A 734 THR cc_start: 0.8899 (m) cc_final: 0.8571 (p) REVERT: A 740 MET cc_start: 0.8233 (ttt) cc_final: 0.8004 (mtp) REVERT: A 817 PHE cc_start: 0.8684 (t80) cc_final: 0.8358 (t80) REVERT: B 237 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6440 (ttm170) REVERT: B 269 TYR cc_start: 0.7441 (m-10) cc_final: 0.7234 (m-80) REVERT: B 271 GLN cc_start: 0.7576 (mt0) cc_final: 0.6984 (mm110) REVERT: B 389 ASP cc_start: 0.7806 (m-30) cc_final: 0.7122 (t70) REVERT: B 417 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7395 (mtpt) REVERT: B 427 ASP cc_start: 0.6542 (m-30) cc_final: 0.6276 (m-30) REVERT: B 507 PRO cc_start: 0.5958 (Cg_exo) cc_final: 0.5687 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6182 (m-80) cc_final: 0.5543 (m-80) REVERT: C 140 PHE cc_start: 0.6182 (p90) cc_final: 0.5632 (p90) REVERT: C 237 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7389 (mtm110) REVERT: C 357 ARG cc_start: 0.7348 (ttp80) cc_final: 0.6818 (tpt90) REVERT: C 427 ASP cc_start: 0.6204 (m-30) cc_final: 0.5582 (t70) REVERT: C 508 TYR cc_start: 0.6663 (m-80) cc_final: 0.6398 (m-80) REVERT: C 569 ILE cc_start: 0.7186 (tp) cc_final: 0.6531 (mm) REVERT: C 755 GLN cc_start: 0.8392 (mt0) cc_final: 0.8005 (mm110) REVERT: C 986 PRO cc_start: 0.7225 (Cg_endo) cc_final: 0.6955 (Cg_endo) REVERT: C 1081 ILE cc_start: 0.8015 (pt) cc_final: 0.7718 (pt) REVERT: C 1144 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: F 34 MET cc_start: 0.1634 (mpp) cc_final: 0.0052 (ttp) REVERT: D 12 MET cc_start: -0.0460 (ptp) cc_final: -0.0718 (ptp) REVERT: E 34 MET cc_start: 0.4816 (mtm) cc_final: 0.4185 (mtm) outliers start: 52 outliers final: 43 residues processed: 288 average time/residue: 0.1714 time to fit residues: 80.7698 Evaluate side-chains 283 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 10.0000 chunk 171 optimal weight: 0.0870 chunk 124 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 112 optimal weight: 0.0030 chunk 172 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 HIS ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.205090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165018 restraints weight = 59850.840| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.59 r_work: 0.3143 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27536 Z= 0.099 Angle : 0.531 15.751 37607 Z= 0.267 Chirality : 0.043 0.332 4431 Planarity : 0.003 0.049 4719 Dihedral : 4.365 46.949 3611 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.41 % Allowed : 11.89 % Favored : 86.70 % 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: 0.37 (0.14), residues: 3290 helix: 2.14 (0.21), residues: 634 sheet: 0.19 (0.17), residues: 861 loop : -0.38 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.018 0.001 TYR E 95 PHE 0.024 0.001 PHE C 400 TRP 0.014 0.001 TRP D 36 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (27425) covalent geometry : angle 0.50268 / 0.26 (37319) SS BOND : bond 0.00325 / 0.22 ( 45) SS BOND : angle 1.38071 / 0.83 ( 90) hydrogen bonds : bond 0.03539 / 2.28 ( 1163) hydrogen bonds : angle 5.33244 / 3.59 ( 3153) link_BETA1-4 : bond 0.00404 / 0.21 ( 20) link_BETA1-4 : angle 1.00669 / 0.68 ( 60) link_NAG-ASN : bond 0.00367 / 0.25 ( 46) link_NAG-ASN : angle 2.62952 / 2.03 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6056 (mmt90) cc_final: 0.5621 (ttt90) REVERT: A 129 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6903 (ptpp) REVERT: A 165 ASN cc_start: 0.5216 (m-40) cc_final: 0.4565 (t0) REVERT: A 230 PRO cc_start: 0.7299 (Cg_endo) cc_final: 0.6875 (Cg_exo) REVERT: A 269 TYR cc_start: 0.7915 (m-80) cc_final: 0.7696 (m-80) REVERT: A 734 THR cc_start: 0.8982 (m) cc_final: 0.8658 (p) REVERT: A 740 MET cc_start: 0.8235 (ttt) cc_final: 0.7992 (mtp) REVERT: A 817 PHE cc_start: 0.8584 (t80) cc_final: 0.8183 (t80) REVERT: B 237 ARG cc_start: 0.6982 (ttp-170) cc_final: 0.6370 (ttm170) REVERT: B 269 TYR cc_start: 0.7402 (m-10) cc_final: 0.7171 (m-80) REVERT: B 271 GLN cc_start: 0.7532 (mt0) cc_final: 0.6888 (mm110) REVERT: B 389 ASP cc_start: 0.7798 (m-30) cc_final: 0.7049 (t70) REVERT: B 417 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7362 (mtpt) REVERT: B 427 ASP cc_start: 0.6597 (m-30) cc_final: 0.6311 (m-30) REVERT: B 507 PRO cc_start: 0.5961 (Cg_exo) cc_final: 0.5698 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6180 (m-80) cc_final: 0.5461 (m-80) REVERT: C 140 PHE cc_start: 0.6052 (p90) cc_final: 0.5469 (p90) REVERT: C 237 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7317 (mtm110) REVERT: C 357 ARG cc_start: 0.7249 (ttp80) cc_final: 0.6947 (tpt-90) REVERT: C 427 ASP cc_start: 0.6258 (m-30) cc_final: 0.5537 (t70) REVERT: C 508 TYR cc_start: 0.6686 (m-80) cc_final: 0.6467 (m-80) REVERT: C 569 ILE cc_start: 0.7274 (tp) cc_final: 0.6618 (mm) REVERT: C 675 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7125 (mm-40) REVERT: C 697 MET cc_start: 0.8475 (ptm) cc_final: 0.8221 (ptp) REVERT: C 755 GLN cc_start: 0.8385 (mt0) cc_final: 0.7951 (mm110) REVERT: C 986 PRO cc_start: 0.7090 (Cg_endo) cc_final: 0.6826 (Cg_endo) REVERT: C 1081 ILE cc_start: 0.7956 (pt) cc_final: 0.7664 (pt) REVERT: C 1144 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: F 34 MET cc_start: 0.1590 (mpp) cc_final: -0.0041 (ttp) REVERT: D 12 MET cc_start: -0.0756 (ptp) cc_final: -0.1281 (ptp) REVERT: D 34 MET cc_start: 0.1875 (OUTLIER) cc_final: 0.1106 (ptt) REVERT: E 34 MET cc_start: 0.4769 (mtm) cc_final: 0.4127 (mtm) outliers start: 37 outliers final: 28 residues processed: 276 average time/residue: 0.1687 time to fit residues: 75.7950 Evaluate side-chains 262 residues out of total 2887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain D residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 219 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.203481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163825 restraints weight = 68597.050| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.87 r_work: 0.3368 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27536 Z= 0.146 Angle : 0.570 15.418 37607 Z= 0.282 Chirality : 0.044 0.289 4431 Planarity : 0.004 0.045 4719 Dihedral : 4.333 47.045 3606 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.73 % Allowed : 11.57 % Favored : 86.70 % 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: 0.33 (0.14), residues: 3290 helix: 2.00 (0.21), residues: 645 sheet: 0.21 (0.17), residues: 845 loop : -0.40 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.019 0.001 TYR E 95 PHE 0.030 0.001 PHE A 643 TRP 0.012 0.001 TRP B 436 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (27425) covalent geometry : angle 0.53733 / 0.27 (37319) SS BOND : bond 0.00392 / 0.25 ( 45) SS BOND : angle 1.56992 / 0.92 ( 90) hydrogen bonds : bond 0.03841 / 2.49 ( 1163) hydrogen bonds : angle 5.37655 / 3.62 ( 3153) link_BETA1-4 : bond 0.00393 / 0.20 ( 20) link_BETA1-4 : angle 1.06134 / 0.72 ( 60) link_NAG-ASN : bond 0.00388 / 0.26 ( 46) link_NAG-ASN : angle 2.88802 / 2.12 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.82 seconds wall clock time: 132 minutes 17.50 seconds (7937.50 seconds total)