Starting phenix.real_space_refine on Sat Jul 4 03:31:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lpn_23480/07_2026/7lpn_23480.map" } resolution = 3.61 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= 0.016 sd= 0.107 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 11094 2.51 5 N 2961 2.21 5 O 3609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s 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: 17787 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 965 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.11, per 1000 atoms: 0.23 Number of scatterers: 17787 At special positions: 0 Unit cell: (130.442, 132.563, 120.897, 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 3609 8.00 N 2961 7.00 C 11094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA a 3 " - " MAN a 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 j 2 " - " BMA j 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 137 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 363 " " NAG C 609 " - " ASN C 160 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 276 " " NAG F 604 " - " ASN F 339 " " NAG F 605 " - " ASN F 355 " " NAG F 606 " - " ASN F 137 " " NAG F 607 " - " ASN F 448 " " NAG F 608 " - " ASN F 363 " " NAG F 609 " - " ASN F 160 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 137 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 363 " " NAG G 609 " - " ASN G 160 " " NAG J 1 " - " ASN G 156 " " NAG K 1 " - " ASN G 197 " " NAG L 1 " - " ASN G 234 " " NAG M 1 " - " ASN G 295 " " NAG N 1 " - " ASN G 301 " " NAG O 1 " - " ASN G 332 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 392 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 234 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 386 " " NAG Z 1 " - " ASN C 392 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 234 " " NAG e 1 " - " ASN F 295 " " NAG f 1 " - " ASN F 301 " " NAG g 1 " - " ASN F 332 " " NAG h 1 " - " ASN F 386 " " NAG i 1 " - " ASN F 392 " " NAG j 1 " - " ASN F 262 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 685.6 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3852 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 36 sheets defined 21.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.643A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.877A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.003A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.645A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 641 through 661 removed outlier: 3.654A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.552A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.733A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100C through 100E No H-bonds generated for 'chain 'H' and resid 100C through 100E' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.686A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 Processing helix chain 'A' and resid 611 through 616 removed outlier: 3.960A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.587A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.668A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.587A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.188A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.671A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.218A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.710A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.184A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.970A pdb=" N GLN D 31 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 100C through 100E No H-bonds generated for 'chain 'D' and resid 100C through 100E' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 538 through 543 removed outlier: 3.828A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.148A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.544A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 637 removed outlier: 3.644A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 661 Processing helix chain 'F' and resid 99 through 115 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.669A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 481 removed outlier: 4.085A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.701A pdb=" N GLN I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 100C through 100E No H-bonds generated for 'chain 'I' and resid 100C through 100E' Processing sheet with id=AA1, first strand: chain 'B' and resid 604 through 609 removed outlier: 3.525A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.693A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.729A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.777A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.777A pdb=" N ARG G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.131A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.061A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 34 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.061A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.861A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.230A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.656A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.683A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.415A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.000A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.520A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 360 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.674A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AC4, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.502A pdb=" N VAL D 5 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR D 110 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 34 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR D 110 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 604 through 609 removed outlier: 3.511A pdb=" N CYS E 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL F 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.744A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.710A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AD2, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.548A pdb=" N ARG F 273 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.548A pdb=" N ARG F 273 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.668A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.691A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.503A pdb=" N VAL I 5 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.775A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET I 34 " --> pdb=" O MET I 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.775A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET I 34 " --> pdb=" O MET I 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1431 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: 3.37 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5580 1.35 - 1.47: 4613 1.47 - 1.59: 7765 1.59 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 18126 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" N GLU I 1 " pdb=" CA GLU I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLU D 1 " pdb=" CA GLU D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 18121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 23917 1.89 - 3.77: 527 3.77 - 5.66: 103 5.66 - 7.54: 20 7.54 - 9.43: 3 Bond angle restraints: 24570 Sorted by residual: angle pdb=" N SER I 97 " pdb=" CA SER I 97 " pdb=" C SER I 97 " ideal model delta sigma weight residual 107.49 113.32 -5.83 1.74e+00 3.30e-01 1.12e+01 angle pdb=" CA LEU F 494 " pdb=" CB LEU F 494 " pdb=" CG LEU F 494 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.25e+00 angle pdb=" CA CYS F 54 " pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " ideal model delta sigma weight residual 114.40 120.55 -6.15 2.30e+00 1.89e-01 7.14e+00 angle pdb=" N LEU A 544 " pdb=" CA LEU A 544 " pdb=" C LEU A 544 " ideal model delta sigma weight residual 114.04 110.77 3.27 1.24e+00 6.50e-01 6.97e+00 angle pdb=" CA LEU G 494 " pdb=" CB LEU G 494 " pdb=" CG LEU G 494 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 ... (remaining 24565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 8963 16.64 - 33.28: 918 33.28 - 49.92: 170 49.92 - 66.56: 18 66.56 - 83.20: 11 Dihedral angle restraints: 10080 sinusoidal: 4101 harmonic: 5979 Sorted by residual: dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -26.75 -59.25 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.73 55.73 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -141.35 55.35 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2517 0.055 - 0.109: 367 0.109 - 0.164: 129 0.164 - 0.219: 5 0.219 - 0.273: 12 Chirality restraints: 3030 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3027 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 571 " -0.014 2.00e-02 2.50e+03 1.03e-02 2.67e+00 pdb=" CG TRP A 571 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 571 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 571 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 571 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 571 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 571 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 571 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 571 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 571 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 69 " -0.011 2.00e-02 2.50e+03 9.12e-03 2.08e+00 pdb=" CG TRP G 69 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 69 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP G 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 69 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 69 " -0.013 2.00e-02 2.50e+03 8.76e-03 1.92e+00 pdb=" CG TRP C 69 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 69 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP C 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 69 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 69 " -0.003 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 386 2.66 - 3.22: 16864 3.22 - 3.78: 24668 3.78 - 4.34: 33616 4.34 - 4.90: 55177 Nonbonded interactions: 130711 Sorted by model distance: nonbonded pdb=" O3 NAG Q 1 " pdb=" O5 NAG Q 2 " model vdw 2.103 3.040 nonbonded pdb=" O3 NAG Z 1 " pdb=" O5 NAG Z 2 " model vdw 2.112 3.040 nonbonded pdb=" O3 NAG i 1 " pdb=" O5 NAG i 2 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.135 3.040 nonbonded pdb=" OG SER F 460 " pdb=" OD1 ASN F 462 " model vdw 2.145 3.040 ... (remaining 130706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'S' selection = chain 'T' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'W' selection = chain 'a' selection = chain 'f' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.004 0.039 18270 Z= 0.215 Angle : 0.678 9.426 24963 Z= 0.293 Chirality : 0.049 0.273 3030 Planarity : 0.002 0.024 3003 Dihedral : 13.090 83.203 6111 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 2040 helix: 1.20 (0.32), residues: 342 sheet: -0.51 (0.25), residues: 459 loop : -1.05 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 105 TYR 0.004 0.001 TYR C 486 PHE 0.009 0.001 PHE C 288 TRP 0.028 0.001 TRP A 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (18126) covalent geometry : angle 0.66062 / 0.29 (24570) SS BOND : bond 0.00317 / 0.18 ( 39) SS BOND : angle 0.85378 / 0.56 ( 78) hydrogen bonds : bond 0.26944 / 18.22 ( 504) hydrogen bonds : angle 8.76505 / 6.25 ( 1431) link_ALPHA1-3 : bond 0.00406 / 0.20 ( 3) link_ALPHA1-3 : angle 1.59405 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 3) link_ALPHA1-6 : angle 1.48740 / 0.73 ( 9) link_BETA1-4 : bond 0.00534 / 0.33 ( 39) link_BETA1-4 : angle 1.91199 / 1.32 ( 117) link_NAG-ASN : bond 0.00158 / 0.11 ( 60) link_NAG-ASN : angle 1.08685 / 0.68 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: B 543 ASN cc_start: 0.8910 (t0) cc_final: 0.8623 (t0) REVERT: B 647 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 195 ASN cc_start: 0.8149 (p0) cc_final: 0.7835 (p0) REVERT: A 543 ASN cc_start: 0.8850 (t0) cc_final: 0.8477 (t0) REVERT: A 584 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 647 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 648 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 654 GLU cc_start: 0.8654 (tp30) cc_final: 0.8408 (tp30) REVERT: D 44 GLU cc_start: 0.8400 (mp0) cc_final: 0.8176 (mp0) REVERT: E 543 ASN cc_start: 0.8689 (t0) cc_final: 0.8295 (t0) REVERT: E 584 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8282 (tm-30) REVERT: E 647 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7850 (tm-30) REVERT: E 648 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 434 MET cc_start: 0.8500 (ttm) cc_final: 0.8227 (ttm) REVERT: I 44 GLU cc_start: 0.8415 (mp0) cc_final: 0.8179 (mp0) REVERT: I 82 MET cc_start: 0.8466 (mmp) cc_final: 0.8014 (mmp) outliers start: 4 outliers final: 3 residues processed: 192 average time/residue: 0.1212 time to fit residues: 36.4877 Evaluate side-chains 138 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain I residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 GLN A 616 ASN C 103 GLN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.059733 restraints weight = 48721.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.062246 restraints weight = 25559.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063894 restraints weight = 17549.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064970 restraints weight = 13987.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.065674 restraints weight = 12101.449| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18270 Z= 0.176 Angle : 0.632 12.341 24963 Z= 0.309 Chirality : 0.044 0.174 3030 Planarity : 0.003 0.034 3003 Dihedral : 4.331 22.241 2232 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.55 % Allowed : 7.38 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 2040 helix: 0.92 (0.29), residues: 363 sheet: -0.96 (0.25), residues: 420 loop : -1.10 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.010 0.001 TYR C 173 PHE 0.025 0.002 PHE D 17 TRP 0.023 0.002 TRP A 571 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (18126) covalent geometry : angle 0.60467 / 0.30 (24570) SS BOND : bond 0.00315 / 0.19 ( 39) SS BOND : angle 0.96996 / 0.62 ( 78) hydrogen bonds : bond 0.05841 / 3.85 ( 504) hydrogen bonds : angle 6.23056 / 4.49 ( 1431) link_ALPHA1-3 : bond 0.00567 / 0.29 ( 3) link_ALPHA1-3 : angle 1.59690 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00488 / 0.24 ( 3) link_ALPHA1-6 : angle 1.56765 / 0.76 ( 9) link_BETA1-4 : bond 0.00580 / 0.35 ( 39) link_BETA1-4 : angle 2.12868 / 1.42 ( 117) link_NAG-ASN : bond 0.00285 / 0.20 ( 60) link_NAG-ASN : angle 1.37262 / 0.90 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.697 Fit side-chains REVERT: B 543 ASN cc_start: 0.8952 (t0) cc_final: 0.8447 (t0) REVERT: B 584 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 647 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 654 GLU cc_start: 0.9200 (tp30) cc_final: 0.8948 (tp30) REVERT: A 530 MET cc_start: 0.8243 (ttp) cc_final: 0.7979 (ttt) REVERT: A 543 ASN cc_start: 0.8952 (t0) cc_final: 0.8406 (t0) REVERT: A 584 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 647 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 648 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8783 (mm-30) REVERT: A 654 GLU cc_start: 0.8927 (tp30) cc_final: 0.8719 (tp30) REVERT: D 44 GLU cc_start: 0.8503 (mp0) cc_final: 0.8266 (mp0) REVERT: E 543 ASN cc_start: 0.8820 (t0) cc_final: 0.8253 (t0) REVERT: E 647 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8246 (tm-30) REVERT: E 648 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8784 (mm-30) REVERT: F 426 MET cc_start: 0.8497 (ptm) cc_final: 0.8264 (ptm) REVERT: F 434 MET cc_start: 0.8436 (ttm) cc_final: 0.8110 (ttm) REVERT: I 44 GLU cc_start: 0.8508 (mp0) cc_final: 0.8252 (mp0) REVERT: I 82 MET cc_start: 0.8284 (mmp) cc_final: 0.7624 (mmp) outliers start: 10 outliers final: 6 residues processed: 148 average time/residue: 0.1166 time to fit residues: 27.3361 Evaluate side-chains 134 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 14 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.056686 restraints weight = 49795.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.059102 restraints weight = 26301.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.060677 restraints weight = 18170.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.061702 restraints weight = 14579.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.062235 restraints weight = 12703.326| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 18270 Z= 0.285 Angle : 0.699 12.333 24963 Z= 0.343 Chirality : 0.046 0.237 3030 Planarity : 0.004 0.034 3003 Dihedral : 4.666 25.698 2229 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.16 % Allowed : 10.80 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 2040 helix: 0.72 (0.28), residues: 363 sheet: -0.61 (0.24), residues: 465 loop : -1.42 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.022 0.001 TYR H 100G PHE 0.022 0.002 PHE C 288 TRP 0.016 0.002 TRP A 571 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 (18126) covalent geometry : angle 0.67158 / 0.34 (24570) SS BOND : bond 0.00494 / 0.30 ( 39) SS BOND : angle 1.35216 / 0.88 ( 78) hydrogen bonds : bond 0.05124 / 3.39 ( 504) hydrogen bonds : angle 5.76665 / 4.15 ( 1431) link_ALPHA1-3 : bond 0.00272 / 0.14 ( 3) link_ALPHA1-3 : angle 1.63259 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00677 / 0.34 ( 3) link_ALPHA1-6 : angle 1.28261 / 0.61 ( 9) link_BETA1-4 : bond 0.00529 / 0.32 ( 39) link_BETA1-4 : angle 1.97193 / 1.31 ( 117) link_NAG-ASN : bond 0.00411 / 0.29 ( 60) link_NAG-ASN : angle 1.62357 / 1.07 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.533 Fit side-chains REVERT: B 543 ASN cc_start: 0.8951 (t0) cc_final: 0.8404 (t0) REVERT: B 584 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 647 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 654 GLU cc_start: 0.9215 (tp30) cc_final: 0.9007 (tp30) REVERT: H 51 MET cc_start: 0.8052 (tpt) cc_final: 0.7809 (tpt) REVERT: H 72 ASP cc_start: 0.7239 (t0) cc_final: 0.6973 (t0) REVERT: A 543 ASN cc_start: 0.8935 (t0) cc_final: 0.8382 (t0) REVERT: A 584 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 647 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 648 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 654 GLU cc_start: 0.9025 (tp30) cc_final: 0.8770 (tp30) REVERT: C 210 PHE cc_start: 0.9295 (m-10) cc_final: 0.9077 (m-10) REVERT: C 416 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6795 (pp) REVERT: D 13 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 44 GLU cc_start: 0.8404 (mp0) cc_final: 0.8173 (mp0) REVERT: D 72 ASP cc_start: 0.7204 (t0) cc_final: 0.6970 (t0) REVERT: E 543 ASN cc_start: 0.8853 (t0) cc_final: 0.8241 (t0) REVERT: E 584 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7908 (tm-30) REVERT: E 647 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8420 (tm-30) REVERT: I 34 MET cc_start: 0.9269 (mmm) cc_final: 0.9063 (mmm) REVERT: I 44 GLU cc_start: 0.8540 (mp0) cc_final: 0.8292 (mp0) REVERT: I 82 MET cc_start: 0.8662 (mmp) cc_final: 0.7942 (mmp) outliers start: 21 outliers final: 10 residues processed: 149 average time/residue: 0.1061 time to fit residues: 25.4023 Evaluate side-chains 134 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.058945 restraints weight = 48847.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.061446 restraints weight = 25606.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063096 restraints weight = 17610.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064176 restraints weight = 14057.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064837 restraints weight = 12177.650| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18270 Z= 0.119 Angle : 0.573 12.524 24963 Z= 0.278 Chirality : 0.043 0.163 3030 Planarity : 0.003 0.033 3003 Dihedral : 4.433 22.998 2229 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.60 % Allowed : 11.57 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2040 helix: 1.02 (0.29), residues: 360 sheet: -0.73 (0.24), residues: 438 loop : -1.25 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.018 0.001 TYR H 100G PHE 0.027 0.001 PHE D 17 TRP 0.023 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (18126) covalent geometry : angle 0.54874 / 0.27 (24570) SS BOND : bond 0.00226 / 0.15 ( 39) SS BOND : angle 0.80831 / 0.53 ( 78) hydrogen bonds : bond 0.03982 / 2.64 ( 504) hydrogen bonds : angle 5.24548 / 3.80 ( 1431) link_ALPHA1-3 : bond 0.00533 / 0.27 ( 3) link_ALPHA1-3 : angle 1.38387 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00537 / 0.27 ( 3) link_ALPHA1-6 : angle 1.26339 / 0.61 ( 9) link_BETA1-4 : bond 0.00492 / 0.30 ( 39) link_BETA1-4 : angle 1.81103 / 1.19 ( 117) link_NAG-ASN : bond 0.00203 / 0.14 ( 60) link_NAG-ASN : angle 1.38188 / 0.90 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.609 Fit side-chains REVERT: B 543 ASN cc_start: 0.8948 (t0) cc_final: 0.8373 (t0) REVERT: B 584 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 647 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 654 GLU cc_start: 0.9194 (tp30) cc_final: 0.8971 (tp30) REVERT: G 47 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: G 271 MET cc_start: 0.7883 (mmm) cc_final: 0.7648 (mmm) REVERT: A 543 ASN cc_start: 0.8918 (t0) cc_final: 0.8351 (t0) REVERT: A 574 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8074 (ptmt) REVERT: A 584 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 633 LYS cc_start: 0.9184 (mttp) cc_final: 0.8904 (mptt) REVERT: A 647 GLU cc_start: 0.8685 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 648 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8742 (mm-30) REVERT: C 47 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: C 95 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7637 (ptp) REVERT: C 161 MET cc_start: 0.8157 (tpp) cc_final: 0.7934 (tpp) REVERT: C 210 PHE cc_start: 0.9245 (m-10) cc_final: 0.9004 (m-10) REVERT: C 475 MET cc_start: 0.8581 (tpp) cc_final: 0.8369 (tpp) REVERT: D 44 GLU cc_start: 0.8389 (mp0) cc_final: 0.8131 (mp0) REVERT: E 543 ASN cc_start: 0.8848 (t0) cc_final: 0.8214 (t0) REVERT: E 584 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7906 (tm-30) REVERT: E 647 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8442 (tm-30) REVERT: F 47 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: I 34 MET cc_start: 0.9314 (mmm) cc_final: 0.9000 (mmm) REVERT: I 82 MET cc_start: 0.8677 (mmp) cc_final: 0.8045 (mmp) outliers start: 29 outliers final: 17 residues processed: 163 average time/residue: 0.1092 time to fit residues: 28.5654 Evaluate side-chains 150 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 149 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 119 optimal weight: 0.0170 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 206 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.059694 restraints weight = 48067.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.062238 restraints weight = 25394.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063902 restraints weight = 17489.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064975 restraints weight = 13995.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.065639 restraints weight = 12135.744| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18270 Z= 0.110 Angle : 0.562 11.935 24963 Z= 0.271 Chirality : 0.043 0.162 3030 Planarity : 0.003 0.034 3003 Dihedral : 4.300 22.645 2229 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.20 % Allowed : 12.84 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2040 helix: 1.22 (0.29), residues: 357 sheet: -0.31 (0.23), residues: 483 loop : -1.34 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.027 0.001 TYR H 100G PHE 0.027 0.001 PHE H 17 TRP 0.024 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18126) covalent geometry : angle 0.53817 / 0.27 (24570) SS BOND : bond 0.00213 / 0.14 ( 39) SS BOND : angle 0.97142 / 0.61 ( 78) hydrogen bonds : bond 0.03601 / 2.39 ( 504) hydrogen bonds : angle 5.00089 / 3.64 ( 1431) link_ALPHA1-3 : bond 0.00520 / 0.26 ( 3) link_ALPHA1-3 : angle 1.38128 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00493 / 0.25 ( 3) link_ALPHA1-6 : angle 1.28147 / 0.62 ( 9) link_BETA1-4 : bond 0.00502 / 0.30 ( 39) link_BETA1-4 : angle 1.74902 / 1.15 ( 117) link_NAG-ASN : bond 0.00200 / 0.14 ( 60) link_NAG-ASN : angle 1.30547 / 0.85 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.695 Fit side-chains REVERT: B 543 ASN cc_start: 0.8883 (t0) cc_final: 0.8301 (t0) REVERT: B 584 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 633 LYS cc_start: 0.9216 (mttp) cc_final: 0.9004 (mptt) REVERT: B 647 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 654 GLU cc_start: 0.9163 (tp30) cc_final: 0.8935 (tp30) REVERT: G 47 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: H 100 TYR cc_start: 0.9098 (m-80) cc_final: 0.8837 (m-10) REVERT: A 543 ASN cc_start: 0.8917 (t0) cc_final: 0.8337 (t0) REVERT: A 574 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8148 (ptpt) REVERT: A 584 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 633 LYS cc_start: 0.9155 (mttp) cc_final: 0.8950 (mmtm) REVERT: A 647 GLU cc_start: 0.8706 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 648 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8667 (mm-30) REVERT: C 47 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: C 95 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7661 (ptp) REVERT: C 210 PHE cc_start: 0.9216 (m-10) cc_final: 0.8949 (m-10) REVERT: C 271 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7152 (mmm) REVERT: D 44 GLU cc_start: 0.8435 (mp0) cc_final: 0.8161 (mp0) REVERT: E 543 ASN cc_start: 0.8852 (t0) cc_final: 0.8252 (t0) REVERT: E 584 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 647 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8402 (tm-30) REVERT: F 475 MET cc_start: 0.8619 (tpp) cc_final: 0.8371 (tpp) REVERT: I 34 MET cc_start: 0.9332 (mmm) cc_final: 0.9005 (mmm) REVERT: I 82 MET cc_start: 0.8693 (mmp) cc_final: 0.7844 (mmp) outliers start: 40 outliers final: 23 residues processed: 173 average time/residue: 0.1290 time to fit residues: 35.4532 Evaluate side-chains 157 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 204 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.059654 restraints weight = 48209.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062167 restraints weight = 25407.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063824 restraints weight = 17493.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064911 restraints weight = 13944.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.065606 restraints weight = 12076.665| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18270 Z= 0.115 Angle : 0.570 14.153 24963 Z= 0.273 Chirality : 0.043 0.162 3030 Planarity : 0.003 0.033 3003 Dihedral : 4.259 22.574 2229 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.20 % Allowed : 13.66 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.18), residues: 2040 helix: 1.25 (0.29), residues: 360 sheet: -0.35 (0.23), residues: 495 loop : -1.27 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.019 0.001 TYR H 100G PHE 0.024 0.001 PHE H 17 TRP 0.029 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (18126) covalent geometry : angle 0.54762 / 0.27 (24570) SS BOND : bond 0.00204 / 0.13 ( 39) SS BOND : angle 0.91689 / 0.58 ( 78) hydrogen bonds : bond 0.03447 / 2.30 ( 504) hydrogen bonds : angle 4.87003 / 3.54 ( 1431) link_ALPHA1-3 : bond 0.00518 / 0.26 ( 3) link_ALPHA1-3 : angle 1.39677 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00495 / 0.25 ( 3) link_ALPHA1-6 : angle 1.30173 / 0.63 ( 9) link_BETA1-4 : bond 0.00487 / 0.29 ( 39) link_BETA1-4 : angle 1.71651 / 1.12 ( 117) link_NAG-ASN : bond 0.00190 / 0.13 ( 60) link_NAG-ASN : angle 1.28410 / 0.84 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.706 Fit side-chains REVERT: B 543 ASN cc_start: 0.8898 (t0) cc_final: 0.8314 (t0) REVERT: B 584 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 588 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7821 (ttm170) REVERT: B 633 LYS cc_start: 0.9195 (mttp) cc_final: 0.8982 (mptt) REVERT: B 647 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 654 GLU cc_start: 0.9156 (tp30) cc_final: 0.8934 (tp30) REVERT: G 47 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: G 271 MET cc_start: 0.7876 (mmm) cc_final: 0.7669 (mmm) REVERT: A 543 ASN cc_start: 0.8914 (t0) cc_final: 0.8334 (t0) REVERT: A 574 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8100 (ptmt) REVERT: A 584 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 647 GLU cc_start: 0.8714 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 648 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8700 (mm-30) REVERT: C 47 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: C 95 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7748 (ptp) REVERT: C 210 PHE cc_start: 0.9224 (m-10) cc_final: 0.8969 (m-10) REVERT: C 271 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7227 (mmm) REVERT: D 44 GLU cc_start: 0.8429 (mp0) cc_final: 0.8150 (mp0) REVERT: E 543 ASN cc_start: 0.8867 (t0) cc_final: 0.8274 (t0) REVERT: E 584 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7463 (tm-30) REVERT: E 626 MET cc_start: 0.8834 (mtp) cc_final: 0.8291 (ttp) REVERT: E 647 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 47 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: F 475 MET cc_start: 0.8582 (tpp) cc_final: 0.8305 (tpp) REVERT: I 34 MET cc_start: 0.9323 (mmm) cc_final: 0.9018 (mmm) REVERT: I 82 MET cc_start: 0.8563 (mmp) cc_final: 0.7739 (mmp) outliers start: 40 outliers final: 25 residues processed: 175 average time/residue: 0.1351 time to fit residues: 36.9868 Evaluate side-chains 161 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 135 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 122 optimal weight: 0.0370 chunk 196 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 GLN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059921 restraints weight = 48480.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.062460 restraints weight = 25302.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064138 restraints weight = 17289.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065228 restraints weight = 13733.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065797 restraints weight = 11857.415| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18270 Z= 0.111 Angle : 0.568 13.990 24963 Z= 0.272 Chirality : 0.043 0.162 3030 Planarity : 0.003 0.034 3003 Dihedral : 4.229 23.765 2229 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.37 % Allowed : 13.72 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 2040 helix: 1.10 (0.29), residues: 378 sheet: -0.19 (0.24), residues: 486 loop : -1.27 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.011 0.001 TYR H 100G PHE 0.022 0.001 PHE H 17 TRP 0.038 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (18126) covalent geometry : angle 0.54603 / 0.27 (24570) SS BOND : bond 0.00206 / 0.13 ( 39) SS BOND : angle 0.90426 / 0.56 ( 78) hydrogen bonds : bond 0.03320 / 2.22 ( 504) hydrogen bonds : angle 4.76747 / 3.47 ( 1431) link_ALPHA1-3 : bond 0.00515 / 0.26 ( 3) link_ALPHA1-3 : angle 1.39820 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00502 / 0.25 ( 3) link_ALPHA1-6 : angle 1.30913 / 0.63 ( 9) link_BETA1-4 : bond 0.00487 / 0.29 ( 39) link_BETA1-4 : angle 1.68647 / 1.10 ( 117) link_NAG-ASN : bond 0.00184 / 0.13 ( 60) link_NAG-ASN : angle 1.26375 / 0.82 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.691 Fit side-chains REVERT: B 543 ASN cc_start: 0.8911 (t0) cc_final: 0.8326 (t0) REVERT: B 584 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 588 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7711 (ttm170) REVERT: B 633 LYS cc_start: 0.9181 (mttp) cc_final: 0.8965 (mptt) REVERT: B 647 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 654 GLU cc_start: 0.9144 (tp30) cc_final: 0.8917 (tp30) REVERT: G 47 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: G 271 MET cc_start: 0.7988 (mmm) cc_final: 0.7744 (mmm) REVERT: H 51 MET cc_start: 0.8181 (tpt) cc_final: 0.7668 (tpp) REVERT: A 543 ASN cc_start: 0.8919 (t0) cc_final: 0.8340 (t0) REVERT: A 574 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8048 (ptmt) REVERT: A 584 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 647 GLU cc_start: 0.8680 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 648 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8608 (mm-30) REVERT: C 47 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: C 95 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7779 (ptp) REVERT: C 210 PHE cc_start: 0.9190 (m-10) cc_final: 0.8966 (m-10) REVERT: C 475 MET cc_start: 0.8769 (tpp) cc_final: 0.8399 (tpp) REVERT: D 30 ASN cc_start: 0.8906 (p0) cc_final: 0.8463 (p0) REVERT: D 44 GLU cc_start: 0.8422 (mp0) cc_final: 0.8141 (mp0) REVERT: E 543 ASN cc_start: 0.8857 (t0) cc_final: 0.8254 (t0) REVERT: E 584 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7459 (tm-30) REVERT: E 626 MET cc_start: 0.8842 (mtp) cc_final: 0.8525 (ttm) REVERT: F 47 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: F 161 MET cc_start: 0.8012 (mmm) cc_final: 0.7473 (mmm) REVERT: F 374 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.6671 (p-80) REVERT: F 475 MET cc_start: 0.8606 (tpp) cc_final: 0.8318 (tpp) REVERT: I 34 MET cc_start: 0.9353 (mmm) cc_final: 0.9038 (mmm) REVERT: I 82 MET cc_start: 0.8556 (mmp) cc_final: 0.7833 (mmp) outliers start: 43 outliers final: 23 residues processed: 178 average time/residue: 0.1305 time to fit residues: 36.7306 Evaluate side-chains 160 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 72 HIS F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.080814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060455 restraints weight = 48459.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.063021 restraints weight = 25329.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064724 restraints weight = 17303.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065817 restraints weight = 13758.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066418 restraints weight = 11889.586| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18270 Z= 0.102 Angle : 0.568 13.767 24963 Z= 0.270 Chirality : 0.042 0.162 3030 Planarity : 0.003 0.034 3003 Dihedral : 4.143 21.976 2229 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 2040 helix: 1.40 (0.29), residues: 363 sheet: -0.07 (0.23), residues: 495 loop : -1.26 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 105 TYR 0.007 0.001 TYR A 586 PHE 0.020 0.001 PHE H 17 TRP 0.040 0.001 TRP A 571 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (18126) covalent geometry : angle 0.54865 / 0.27 (24570) SS BOND : bond 0.00147 / 0.09 ( 39) SS BOND : angle 0.79328 / 0.50 ( 78) hydrogen bonds : bond 0.03208 / 2.13 ( 504) hydrogen bonds : angle 4.65356 / 3.38 ( 1431) link_ALPHA1-3 : bond 0.00533 / 0.27 ( 3) link_ALPHA1-3 : angle 1.38366 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00460 / 0.23 ( 3) link_ALPHA1-6 : angle 1.30461 / 0.63 ( 9) link_BETA1-4 : bond 0.00488 / 0.30 ( 39) link_BETA1-4 : angle 1.65393 / 1.08 ( 117) link_NAG-ASN : bond 0.00176 / 0.12 ( 60) link_NAG-ASN : angle 1.22330 / 0.80 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 535 MET cc_start: 0.9057 (mmm) cc_final: 0.8822 (mpp) REVERT: B 543 ASN cc_start: 0.8935 (t0) cc_final: 0.8344 (t0) REVERT: B 584 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 588 ARG cc_start: 0.8271 (tpp80) cc_final: 0.7745 (ttm170) REVERT: B 633 LYS cc_start: 0.9167 (mttp) cc_final: 0.8960 (mptt) REVERT: B 647 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8342 (tm-30) REVERT: B 654 GLU cc_start: 0.9130 (tp30) cc_final: 0.8908 (tp30) REVERT: G 47 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8101 (m-30) REVERT: G 271 MET cc_start: 0.8027 (mmm) cc_final: 0.7778 (mmm) REVERT: H 83 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8375 (mmtt) REVERT: A 543 ASN cc_start: 0.8901 (t0) cc_final: 0.8377 (t0) REVERT: A 574 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8059 (ptmt) REVERT: A 584 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 647 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 648 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8758 (mm-30) REVERT: C 47 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: C 161 MET cc_start: 0.8283 (tpp) cc_final: 0.7963 (tpp) REVERT: C 210 PHE cc_start: 0.9151 (m-10) cc_final: 0.8920 (m-10) REVERT: C 475 MET cc_start: 0.8719 (tpp) cc_final: 0.8374 (tpp) REVERT: D 30 ASN cc_start: 0.8891 (p0) cc_final: 0.8456 (p0) REVERT: D 44 GLU cc_start: 0.8409 (mp0) cc_final: 0.8127 (mp0) REVERT: E 543 ASN cc_start: 0.8826 (t0) cc_final: 0.8161 (t0) REVERT: E 584 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7477 (tm-30) REVERT: E 626 MET cc_start: 0.8758 (mtp) cc_final: 0.8414 (ttm) REVERT: F 47 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: F 374 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6454 (p-80) REVERT: F 475 MET cc_start: 0.8607 (tpp) cc_final: 0.8299 (tpp) REVERT: I 34 MET cc_start: 0.9354 (mmm) cc_final: 0.9026 (mmm) REVERT: I 82 MET cc_start: 0.8547 (mmp) cc_final: 0.7858 (mmp) outliers start: 33 outliers final: 26 residues processed: 175 average time/residue: 0.1324 time to fit residues: 36.3518 Evaluate side-chains 166 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 28 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 161 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 151 optimal weight: 0.0980 chunk 56 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.079721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.059379 restraints weight = 48357.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061892 restraints weight = 25345.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063541 restraints weight = 17404.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064612 restraints weight = 13874.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065301 restraints weight = 12018.531| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18270 Z= 0.144 Angle : 0.601 14.971 24963 Z= 0.284 Chirality : 0.043 0.170 3030 Planarity : 0.003 0.034 3003 Dihedral : 4.204 23.013 2229 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.04 % Allowed : 15.21 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 2040 helix: 1.39 (0.29), residues: 363 sheet: -0.11 (0.24), residues: 486 loop : -1.24 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.005 0.001 TYR E 586 PHE 0.028 0.001 PHE H 17 TRP 0.033 0.001 TRP A 571 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (18126) covalent geometry : angle 0.58084 / 0.28 (24570) SS BOND : bond 0.00296 / 0.18 ( 39) SS BOND : angle 0.96498 / 0.62 ( 78) hydrogen bonds : bond 0.03388 / 2.25 ( 504) hydrogen bonds : angle 4.69441 / 3.41 ( 1431) link_ALPHA1-3 : bond 0.00437 / 0.22 ( 3) link_ALPHA1-3 : angle 1.45261 / 0.68 ( 9) link_ALPHA1-6 : bond 0.00532 / 0.27 ( 3) link_ALPHA1-6 : angle 1.32895 / 0.64 ( 9) link_BETA1-4 : bond 0.00475 / 0.29 ( 39) link_BETA1-4 : angle 1.66552 / 1.09 ( 117) link_NAG-ASN : bond 0.00203 / 0.14 ( 60) link_NAG-ASN : angle 1.28318 / 0.83 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.702 Fit side-chains REVERT: B 543 ASN cc_start: 0.8949 (t0) cc_final: 0.8364 (t0) REVERT: B 584 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 588 ARG cc_start: 0.8271 (tpp80) cc_final: 0.7762 (ttm170) REVERT: B 633 LYS cc_start: 0.9155 (mttp) cc_final: 0.8951 (mptt) REVERT: B 647 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8344 (tm-30) REVERT: G 47 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: G 271 MET cc_start: 0.7967 (mmm) cc_final: 0.7730 (mmm) REVERT: H 51 MET cc_start: 0.8186 (tpt) cc_final: 0.7691 (tpp) REVERT: H 83 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8414 (mmtt) REVERT: A 543 ASN cc_start: 0.8917 (t0) cc_final: 0.8397 (t0) REVERT: A 574 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8099 (ptmt) REVERT: A 584 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 647 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 648 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8723 (mm-30) REVERT: C 47 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: C 161 MET cc_start: 0.8328 (tpp) cc_final: 0.8019 (tpp) REVERT: C 210 PHE cc_start: 0.9174 (m-10) cc_final: 0.8971 (m-10) REVERT: C 475 MET cc_start: 0.8761 (tpp) cc_final: 0.8443 (tpp) REVERT: D 44 GLU cc_start: 0.8421 (mp0) cc_final: 0.8144 (mp0) REVERT: E 543 ASN cc_start: 0.8839 (t0) cc_final: 0.8178 (t0) REVERT: E 584 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 626 MET cc_start: 0.8769 (mtp) cc_final: 0.8438 (ttm) REVERT: F 47 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: F 288 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7940 (p90) REVERT: F 374 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.6942 (p-80) REVERT: I 34 MET cc_start: 0.9350 (mmm) cc_final: 0.9049 (mmm) REVERT: I 82 MET cc_start: 0.8557 (mmp) cc_final: 0.7824 (mmp) outliers start: 37 outliers final: 29 residues processed: 169 average time/residue: 0.1295 time to fit residues: 34.8688 Evaluate side-chains 165 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 288 PHE Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 202 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 432 GLN F 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.060118 restraints weight = 47609.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062638 restraints weight = 25319.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064295 restraints weight = 17526.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.065372 restraints weight = 14036.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066072 restraints weight = 12184.976| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18270 Z= 0.113 Angle : 0.592 15.266 24963 Z= 0.278 Chirality : 0.042 0.160 3030 Planarity : 0.003 0.033 3003 Dihedral : 4.171 22.310 2229 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.98 % Allowed : 15.26 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 2040 helix: 1.43 (0.29), residues: 363 sheet: -0.05 (0.24), residues: 486 loop : -1.22 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.005 0.001 TYR A 638 PHE 0.029 0.001 PHE H 17 TRP 0.033 0.001 TRP A 571 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (18126) covalent geometry : angle 0.57292 / 0.27 (24570) SS BOND : bond 0.00171 / 0.10 ( 39) SS BOND : angle 0.84072 / 0.53 ( 78) hydrogen bonds : bond 0.03223 / 2.15 ( 504) hydrogen bonds : angle 4.61441 / 3.35 ( 1431) link_ALPHA1-3 : bond 0.00498 / 0.25 ( 3) link_ALPHA1-3 : angle 1.40628 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00518 / 0.26 ( 3) link_ALPHA1-6 : angle 1.32654 / 0.64 ( 9) link_BETA1-4 : bond 0.00471 / 0.29 ( 39) link_BETA1-4 : angle 1.62733 / 1.06 ( 117) link_NAG-ASN : bond 0.00173 / 0.12 ( 60) link_NAG-ASN : angle 1.23523 / 0.80 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.659 Fit side-chains REVERT: B 543 ASN cc_start: 0.8943 (t0) cc_final: 0.8351 (t0) REVERT: B 584 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 588 ARG cc_start: 0.8274 (tpp80) cc_final: 0.7761 (ttm170) REVERT: B 633 LYS cc_start: 0.9117 (mttp) cc_final: 0.8893 (mptt) REVERT: B 647 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8345 (tm-30) REVERT: G 47 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: G 271 MET cc_start: 0.8014 (mmm) cc_final: 0.7766 (mmm) REVERT: H 51 MET cc_start: 0.8183 (tpt) cc_final: 0.7684 (tpp) REVERT: H 83 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8449 (mmtt) REVERT: A 543 ASN cc_start: 0.8879 (t0) cc_final: 0.8354 (t0) REVERT: A 574 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8102 (ptpt) REVERT: A 584 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 647 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 648 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8709 (mm-30) REVERT: C 47 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: C 161 MET cc_start: 0.8301 (tpp) cc_final: 0.7988 (tpp) REVERT: C 475 MET cc_start: 0.8733 (tpp) cc_final: 0.8393 (tpp) REVERT: D 30 ASN cc_start: 0.8909 (p0) cc_final: 0.8482 (p0) REVERT: D 44 GLU cc_start: 0.8413 (mp0) cc_final: 0.8134 (mp0) REVERT: E 543 ASN cc_start: 0.8822 (t0) cc_final: 0.8155 (t0) REVERT: E 584 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7586 (tm-30) REVERT: E 626 MET cc_start: 0.8752 (mtp) cc_final: 0.8365 (ttm) REVERT: F 47 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: F 374 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.6789 (p-80) REVERT: F 475 MET cc_start: 0.8674 (tpp) cc_final: 0.8170 (tpp) REVERT: I 34 MET cc_start: 0.9350 (mmm) cc_final: 0.9027 (mmm) REVERT: I 82 MET cc_start: 0.8555 (mmp) cc_final: 0.7813 (mmp) outliers start: 36 outliers final: 29 residues processed: 168 average time/residue: 0.1287 time to fit residues: 34.3703 Evaluate side-chains 165 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 19 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 0.4980 chunk 164 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.059378 restraints weight = 48889.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061890 restraints weight = 25780.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063545 restraints weight = 17728.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064619 restraints weight = 14161.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065302 restraints weight = 12262.737| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18270 Z= 0.140 Angle : 0.605 15.033 24963 Z= 0.286 Chirality : 0.043 0.170 3030 Planarity : 0.003 0.033 3003 Dihedral : 4.209 23.127 2229 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.09 % Allowed : 15.32 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2040 helix: 1.43 (0.29), residues: 363 sheet: -0.08 (0.24), residues: 486 loop : -1.24 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.006 0.001 TYR E 586 PHE 0.028 0.001 PHE H 17 TRP 0.029 0.001 TRP C 479 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (18126) covalent geometry : angle 0.58548 / 0.28 (24570) SS BOND : bond 0.00229 / 0.14 ( 39) SS BOND : angle 1.00428 / 0.62 ( 78) hydrogen bonds : bond 0.03347 / 2.22 ( 504) hydrogen bonds : angle 4.63648 / 3.36 ( 1431) link_ALPHA1-3 : bond 0.00423 / 0.21 ( 3) link_ALPHA1-3 : angle 1.45128 / 0.68 ( 9) link_ALPHA1-6 : bond 0.00532 / 0.27 ( 3) link_ALPHA1-6 : angle 1.33390 / 0.64 ( 9) link_BETA1-4 : bond 0.00462 / 0.28 ( 39) link_BETA1-4 : angle 1.63564 / 1.07 ( 117) link_NAG-ASN : bond 0.00200 / 0.14 ( 60) link_NAG-ASN : angle 1.27491 / 0.83 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.24 seconds wall clock time: 43 minutes 57.34 seconds (2637.34 seconds total)